VrlWiki - User contributions [en]

Diffusion MRI Matlab scripts

2015-08-26T15:46:00Z

Jadrian Miles: Updated directory path to $G from old /map/gfx0

There are many Matlab scripts in <tt>$G/project/brain/pipeline</tt> that are useful for manipulating [[diffusion MRI]] data. These generally fall into two groups: those used in the [[diffusion processing pipeline]] for non-interactive conversion to the VRL in-house [[MRIimage]] format, and those used interactively to inspect and troubleshoot data.

For non-interactive applications, the utility program <tt>matlabLauncher.py</tt> can be used to call a Matlab function with specific arguments from the command line.

* '''Batch Convert''' several files of a given type to [[MRIimage]]
** <tt>processDicoms.m</tt> --- convert from a directory full of single-slice [[DICOM]]s
** <tt>processMosaics.m</tt> --- convert from a directory full of [[DICOM]] Mosaic files
* '''Read''' images in various formats from disk and create Matlab structures from them
** <tt>readMriImage.m</tt> --- read a directory of [[MRIimage]] volumes
** <tt>readMriImageVolume.m</tt> --- read a single of [[MRIimage]] volume
** <tt>readDicomDir.m</tt> --- read a directory of [[DICOM]] images
** <tt>stackFromPattern.m</tt> --- read an arbitrary collection of [[DICOM]] images matching a pattern
** <tt>splitMosaic.m</tt> --- read a single [[DICOM]] mosaic file
** <tt>splitMosaicList.m</tt> --- run <tt>splitMosaic</tt> on each of a list of files
** <tt>readTubegenLineFile.m</tt> --- read a <tt>[[tubegen]]</tt> <tt>.data</tt> or <tt>.nocr</tt> file
* '''Write''' Matlab structures to disk in various formats
** <tt>writeVolumes.m</tt> --- write a collection of Matlab data volumes to [[MRIimage]] and/or [[DICOM]] files
** <tt>writeTubegenLineFile.m</tt> --- write a cell array of three-column Matlab arrays to a <tt>[[tubegen]]</tt> <tt>.nocr</tt> file
* '''Inspect''' and troubleshoot data interactively
** <tt>viewSlice.m</tt> --- show a single 2-D slice of an array with a realistic gamma-corrected monochrome colormap
** <tt>stackToVideo.m</tt> --- show 2-D slices of an array as a video, sweeping the viewing slice along the Z axis
** <tt>makeMriAtlas.m</tt> --- read MRIimage data, generate a mosaic for each volume, and write the mosaics to disk as PNGs
** <tt>stackToMosaic.m</tt> --- flatten an array to 2-D by assembling slices into a tiled 2-D matrix (view the output with <tt>viewSlice</tt>)
** <tt>viewDicomDir.m</tt> --- show all 2-D [[DICOM]] images in a directory as a video
* '''Utility''' functions used in the above
** <tt>getDicomIdentifiers.m</tt> --- get the b-value and gradient ID from the [[DICOM]] header (assuming the Siemens file naming scheme)
** <tt>patternToFileList.m</tt> --- generate a cell array of full paths to non-directory files matching a simple (not regex) path pattern
** <tt>copyType.m</tt> --- change the type (''e.g.'' <tt>uint16</tt> or <tt>double</tt>) of one object to match that of another object
** <tt>searchUpward.m</tt> --- find a file whose name matches a given regular expression in the deepest directory above a specified path
** <tt>strjoin.m</tt> --- join a cell array of strings together into a single string, separated by some delimiter
** <tt>strsplit.m</tt> --- split a single string containing some delimiter into a cell array of delimited strings

=== 3rd Party Scripts ===
* [http://www.mathworks.com/matlabcentral/fileexchange/8797 Tools for NIfTI and ANALYZE images]

[[Category:Diffusion MRI]][[Category:Software]]

CavePainting In The Yurt

2015-05-17T14:11:00Z

Jadrian Miles: /* Demo Scenes */

This page is a place to document the process of running [[CavePainting]] in the Yurt. This includes demo scenes, major issues, and goals.

==Demo Scenes==

The following scenes are useful for testing and demos:

* Jadrian's termite mound (2008)
* Dorian Barill's town scene (2008
* Dorian Barill's library scene (2008).

They include a lot of high-quality content, including text, high-resolution textures, and "largeness". We also have a vague idea of other useful scenes, but they need to be tracked down:
* a zoetrope-like scene of a bat flying (EJ Kalafarski's final project from CS137, Fall 2008)
* a swamp-like scene (Maybe Dorion Barrill's final project? Maybe Trevor O'Brien's first drawing from Fall 2008?)

A large number of scenes are archived on both the Brown CS and CCV filesystems:
* Brown CS: /research/graphics/data/cavepainting
* CCV: /gpfs/data/dhl/cavepainting/

The course materials from CS137 also are a good reference for past work:
* Web: http://cs.brown.edu/courses/csci1370/
* Brown CS: /pro/web/web/courses/cs137

The Brown CS course directory has a ton of content that's not externally available, such as movies, photos, etc .

Adding this command is useful automatically loading art for demos:

<code>-c LoadArtwork=${absolute_path}/${name}.3DArt</code>

==Major issues==

* Crashing
** After a scene has been loaded, it will crash if the wands are not trackable. This may also cause crashes if object occlude the wands from the view of the tracker, but we haven't seen this happen.
* Loading problems
** Textures don't seem to load. Instead, they show up as wireframes. It's not clear why this is happening, but a first test could check if new textures can be added (this would tell us if all textures are broken or just the loading).
** Scenes load quickly the first, but it can be very slow to load subsequent scenes. This is probably due to the high overhead of deleting objects in cavepainting. This problem seems like a crash, as the scene stops updating, but with enough time it should eventually start running again with the newly loaded scene.
* Interaction problems
** Currently keyboard input doesn't work. John says the linux vrg3d server has some issues with keyboards, and the windows server has some stability problems (but keyboard access is okay). This is probably something that can be fixed with come configuration. Ultimately, we'll want a wireless keyboard for use inside the yurt.

===Debugging tips===

List the image files used by a 3DArt file:

<code>strings vortexblue.3DArt | grep 'jpg\|JPG\|png\|PNG' | sort | uniq</code>

==Goals==

* All old scenes files working and no major issues!
* Menu and Interface usable for students in CS137
* Examples of high resolution textures and large scenes that show off the resolution of the cave

CavePainting In The Yurt

2015-05-17T14:05:33Z

Jadrian Miles: /* Demo Scenes */ Added sources of vaguely-remembered scenes

This page is a place to document the process of running [[CavePainting]] in the Yurt. This includes demo scenes, major issues, and goals.

==Demo Scenes==

The following scenes are useful for testing and demos:

* Jadrian's termite mound (2008)
* Dorian Barill's town scene (2008
* Dorian Barill's library scene (2008).

They include a lot of high-quality content, including text, high-resolution textures, and "largeness". We'd also have a vague idea of other useful scenes, but they need to be tracked down:
* a swamp-like scene (Dorion Barrill's final project from CS137, Fall 2008)
* a zoetrope-like scene of a bat flying (EJ Kalafarski's final project from CS137, Fall 2008)

A large number of scenes are archived on both the Brown CS and CCV filesystems:
* Brown CS: /research/graphics/data/cavepainting
* CCV: /gpfs/data/dhl/cavepainting/

The course materials from CS137 also are a good reference for past work:
* Web: http://cs.brown.edu/courses/csci1370/
* Brown CS: /pro/web/web/courses/cs137

The Brown CS course directory has a ton of content that's not externally available, such as movies, photos, etc .

Adding this command is useful automatically loading art for demos:

<code>-c LoadArtwork=${absolute_path}/${name}.3DArt</code>

==Major issues==

* Crashing
** After a scene has been loaded, it will crash if the wands are not trackable. This may also cause crashes if object occlude the wands from the view of the tracker, but we haven't seen this happen.
* Loading problems
** Textures don't seem to load. Instead, they show up as wireframes. It's not clear why this is happening, but a first test could check if new textures can be added (this would tell us if all textures are broken or just the loading).
** Scenes load quickly the first, but it can be very slow to load subsequent scenes. This is probably due to the high overhead of deleting objects in cavepainting. This problem seems like a crash, as the scene stops updating, but with enough time it should eventually start running again with the newly loaded scene.
* Interaction problems
** Currently keyboard input doesn't work. John says the linux vrg3d server has some issues with keyboards, and the windows server has some stability problems (but keyboard access is okay). This is probably something that can be fixed with come configuration. Ultimately, we'll want a wireless keyboard for use inside the yurt.

===Debugging tips===

List the image files used by a 3DArt file:

<code>strings vortexblue.3DArt | grep 'jpg\|JPG\|png\|PNG' | sort | uniq</code>

==Goals==

* All old scenes files working and no major issues!
* Menu and Interface usable for students in CS137
* Examples of high resolution textures and large scenes that show off the resolution of the cave

User:Jadrian Miles

2014-01-27T19:22:03Z

Jadrian Miles: /* Nifty code snippets */ PDF cropping

I started my PhD in CS at Brown in Fall 2006. I work on data processing, measurement, and model reconstruction from [[diffusion MRI]] of the brain.

You can find me elsewhere online:
* [http://cs.brown.edu/~jadrian CS department page]
* [http://vis.cs.brown.edu/organization/people/jadrian.html Visweb profile]
* [http://www.google.com/search?q=jadrian+miles Other places]

There are a number of directories related to me on the CS filesystem, all of which are linked from file:///map/gfx0/users/jadrian

==== Personal Documents ====
* '''Planning Documents'''
** [[/OKRs]] ([[/OKRs/Fall 2012|2012F]]) ([[/OKRs/Summer 2012|2012Sum]]) ([[/OKRs/Spring 2012|2012S]]) ([[/OKRs/Fall 2011|2011F]])
** [[:Image:Jadrian Miles PhD Proposal rev3 2010-09-10.pdf|Thesis proposal (v3, 2010-09-10)]] ([[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|v2, 2009-10-15]]) ([[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|v1, 2009-06-22]])
** [[/Paper list]]
** [[/End-of-PhD cleanup taks]]
* '''Project Notes'''
** [[/Chi-squared clustering]]
** [[/Triangle toy problem]]
** [[/vis2011 tractography statistics paper]]
** [[/Thesis manifesto: probabilistic worldview]]
* '''Archive'''
** [[/PhD Plan]]
** [[/Thesis proposal feedback]]
** [[/Research Projects]]
** [[/Diffusion simulation]]
** [[/Streamline clustering]]
** [[/Cluster slicing notes]]

==== Draft pages / notes ====
* [[/Theory Conference Deadlines]]
* [[/Plan your PhD]]
* [[/Diffusion MRI techniques]]
* [[/BB's dollarg]]
* [[/Eclipse]]
* [[/sandbox]]

==== Nifty code snippets ====
* Generate a random filename from the command line: <pre>set tmpfile=/tmp/`head -q -c 8 /proc/sys/kernel/random/uuid`</pre>
* Convert stdin to lowercase on stdout: <pre>tr '[A-Z]' '[a-z]'</pre>
* Rename files into consecutive zero-padded integers in <tt>bash</tt>: <pre>let i=0; for f in *.JPG; do mv $f `printf "%04d" $i`.jpg; let i++; done</pre>
* Test for host availability in <tt>tcsh</tt> (for loop demo; see [http://www.cyberciti.biz/faq/bash-for-loop/ here] for bash example):
<pre style="margin-left:1.5em">
foreach h ( `cat hostlist` )
ssh $h uname -n
end
</pre>
* Update a directory with stuff that exists in a CVS repository but not in the directory:
*;<pre>cvs update -d</pre>
* Concatenate PDFs (more at [http://web.archive.org/web/20090223000710/http://ansuz.sooke.bc.ca/software/pdf-append.php? the original source]; even more [http://nixtricks.wordpress.com/2009/09/01/cli-combine-or-remove-pages-from-a-pdf-document-using-ghostscript/ elsewhere], as well as [http://www.linuxjournal.com/content/tech-tip-extract-pages-pdf how to extract ranges of pages])
*;<pre>gs -q -sPAPERSIZE=letter -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=out.pdf in1.pdf in2.pdf ...</pre>
* Crop PDF (more at [http://stackoverflow.com/questions/10417151/pdf-remove-white-margins/10418720#10418720 StackOverflow]:
<div style="margin-left: 1.5em">
First, figure out the size of the bounding box:
<pre> gs -q -dBATCH -dNOPAUSE -sDEVICE=bbox orig.pdf 2>&1 | grep -v HiRes
%%BoundingBox: 134 158 471 715
...</pre>
The resulting bounding box is in the form <code>B_x B_y T_x T_y</code>, where B and T are the coordinates of the bottom and top corners, respectively, measured in points.
The bounding box lies on a page of a certain size. One point is 1/72", so letter size is 612x792pt.
In this case, we'd like to leave a 10pt margin on all sides. That means offsetting the page down and left by 124x148pts, and then cropping to a page size of (471-134)+20=357pts wide and (715-158)+20=577pts tall. The command is:
<pre> gs -o cropped.pdf -sDEVICE=pdfwrite -g3570x5770 -c "<</PageOffset [-124 -148]>> setpagedevice" -f orig.pdf</pre>
Note that the argument to <code>-g</code> is in ''tenths'' of a point.
</div>
* Recache TeX search paths: <pre>sudo mktexlsr</pre>
* Perceptually uniform random coloring in Matlab
<pre style="margin-left:1.5em">
C = makecform('lab2srgb');
plot3(X,Y,Z,'Color', applycform([50+rand*50, -100+rand*200, -100+rand*200], C));
</pre>
* Recursively download a website using wget (see [http://www.editcorp.com/Personal/Lars_Appel/wget/wget_2.html#SEC11 the man page] for more) <pre>wget -r -np -nH http://www.site.com/subdir</pre>
* Recursively download a remote directory via SSH, preserving modification times (note the trailing slash on the remote directory!): <pre>rsync -ra -e ssh <server>:<dir>/ <local_path></pre>

==== Bookmarks ====
* [http://when2meet.com when2meet.com] --- lightweight meeting scheduling thingie

==== Tutorials ====
* [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance.htm Covariance] and [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance_matrix.htm covariance matrix]
* [http://www.tommangan.us/Tensors.pdf Tensors], by Thomas Mangan.
* [http://www.cs.ucr.edu/~vbz/resources/quatut.pdf Quaternions], by Ken Shoemake.
* [http://diglib.stanford.edu:8091/~klein/lagrange-multipliers.pdf Lagrange Multipliers], by Dan Klein.

==== Miscellaneous notes ====
* High b sensitizes to short length scale (Assaf & Cohen 1998, 2000).
* The cingulum bundle looks like a long, skinny tube (that wraps around the top and back of the CC) in a gross segmentation, and fibers run along the long axis of this tube for most of this length. Their projections into the GM, though, are actually along the side of the tube, on mid-sagittal gyri. This is a really weird shape when it comes to inferring fiber paths from the bundle shape, so it should be a smoke test for any proposed system.
* Sculpture might be a good choice for the second outside minor course. 3D reasoning, malleable shapes...

Diffusion Processing Pipeline

2014-01-20T01:42:34Z

Jadrian Miles: /* Tips */ input restrictions for Q-ball reconstruction on DTK

The diffusion processing pipeline is a collection of scripts and small programs that we use to turn [[Diffusion MRI|diffusion-weighted MRI]] data from our collaborators into more sophisticated models, typically streamline "tracts" along which we can compute various metrics. We can visualize and interact with the output tractogram with [[Brainapp]]. At the moment, our pipeline is built around DTI --- Diffusion ''Tensor'' Imaging --- but this is not the only thing you can do with diffusion-weighted MRI data, and in the future we may want to turn this pipeline into something that has a few more branches.

Right now little of the code used in the processing pipeline is checked into [[$G]], and those programs that are checked in are usually very small and scattered around the source tree. After Brad's new system is in place, he and Jadrian will work on getting all the scripts we use fixed up and checked into a single location. In the text below, the prefix <code>$dbin</code> means <code>/map/gfx0/common0/diffusion/Interface/bin/data</code>, where a lot of scripts currently live.

{{warning|'''Note:''' if you're running the pipeline for the first time on data from a new protocol, you'll probably discover [[Diagnose tensor orientation problems|orientation problems]] or other issues. It's a real drag to wait around for long processes to complete just to discover that the output is bad. Do yourself a favor and '''do a test run [[Run the diffusion processing pipeline at low resolution|at low resolution]]!'''}}

== Pipeline Steps ==

=== Step 1: Convert from Original Format ===
We receive imaging data in a [[Diffusion MRI#File Formats|variety of different formats]], but we standardize on [[MRIimage]] for all of the programs we write. Therefore we have a few converter programs. We assume that every pipeline starts from this step with DWIs from our collaborators. They may give us files that came more or less directly from the scanner, or they may have done some pre-processing like smoothing, distortion correction, or registration. For example, Ron Cohen's group has started using [[FLIRT]] to register all the DWIs together.

* <code>$dbin/processNiftiDwis.py</code> --- convert from [[NIfTI]] to MRIimage
* <code>$dbin/processMosaics.m</code> (with <code>$dbin/matlabLauncher.py</code>) --- convert from [[DICOM#Mosaic|DICOM Mosaic]] to MRIimage

* <code>$dbin/rotateBvecs.py</code> --- rotate an original list of b vectors to correspond to registration transformations

=== Step 2: Process DWIs ===
Here our scripts take MRIimage DWIs as input and create modified MRIimage DWIs as output. We may upsample, smooth, crop, or pad the images. If we have prior knowledge about orientation issues, we may rotate or flip the images in this step before anything else, so that these operations are as inexpensive as possible in a fully automated process.

* <code>$G/bin/mricrop</code> --- crop or pad images to match a specified voxel volume
* <code>$G/bin/mrifilt3</code> --- resample images to match a specified voxel volume
* <code>$dbin/diffusionResize.py</code> --- by calling the previous two, automatically resample, crop, and pad images to a specified spatial volume in mm, sampled by a specified voxel volume
* <code>$G/bin/mritransp</code> --- permute and/or flip dimensions in a DWI

=== Step 3: Generate (and Possibly Process) Tensors ===
We fit tensors to the DWIs using a nonlinear sequential quadratic programming method; the citation for this process is {{pub|Ahrens-1998-MMT|Ahrens MRM '98}}. In manual runs, we may [[Diagnose tensor orientation problems|discover a tensor orientation issue]] after they are generated, and correct it at the end of this step.

* <code>$dbin/run_mridfit.py</code> (which calls <code>$G/bin/mridfit</code>) --- fit tensors
* <code>$G/bin/mritensormult</code> --- multiply tensors by a specified transformation matrix

=== Step 4: Generate Tensor Metrics ===
We can generate a plethora of scalar metrics from tensors, including FA, trace, and similar things.

* <code>$G/bin/mritensor_v0</code> --- has a huge menu of options; give it the <code><nowiki>--</nowiki></code> argument to see a list

=== Step 5: Generate Streamtubes ===
''See also: [[Tubegen]]''

Most of our studies involve interacting with and computing measures over "streamtubes", integral paths in the field of principle eigenvectors of the diffusion tensors, which we use as a proxy for axon tracts in the brain's white matter. The <tt>[[tubegen]]</tt> program generates a <tt>*.sm</tt> file that [[Brainapp]] uses to visualize the streamtubes.

* <code>$G/bin/tubegen</code>

=== Step 6: Brainapp Compatibility ===
[[Brainapp]], which we use to visualize and interact with the streamtubes, assumes a particular directory structure so it can find the data. Unfortunately, in opposition to the "for humans to read, not computers" principle, this directory structure is a little nonintuitive for the naive human user. As such the latest versions of the pipeline generate output in a nested directory hierarchy using simple, plain-English names so that people can navigate it easily. We must map this structure to Brainapp's expected structure to make the program work right.

* No self-contained script exists right now, just a sequence of commands in a Makefile. Check out <code>$G/data/diffusion/brown3t/cohen_hiv_study.2007.02.07/Makefile.patients</code>.

This step also generates a custom Brainapp config file to open the particular file, so that users don't have to manually edit a config file for each new brain they want to view. In the code below, <code><BRAIN></code> is the path to the root directory where the pipeline was run for this particular brain, ''e.g.'' <code>$G/data/diffusion/brown3t/cohen_hiv_study.2007.02.07/patient003/tubes.2008.07.27</code>.

<pre>
> cd $G/src/brainapp
> obj/brainapp-gcc3-d -f <BRAIN>/brainapp/settings.cfg -f settings-desktop.cfg
</pre>

== Tips ==
* Run jobs on a [[Computing Resources|fast machine]] rather than your workstation or a CS lab machine.
* If you have to do a big batch of datasets, consider [[Run parallel jobs on the Sun Grid Engine|running them in parallel on the grid engine]].
* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>
* DTK is a suite of tools developed by Van Wedeen's group at <abbr title="Massachusetts General Hospital">MGH</abbr> to accomplish the same thing as our processing pipeline: convert input DWIs into a diffusion model, and then perform tractography. DTK implements not only DTI and DTI tractography, but also q-ball and DSI spherical harmonic ODFs and tractography from those. Therefore DTK can be used for comparison in studies where it is appropriate. Trackvis is the streamline viewing program for DTK, analogous to [[Brainapp]]. Both DTK and Trackvis are installed in $G. Note that the DTI fitting algorithm that DTK implements is different than the one we use, and that Trackvis uses its own tractogram file format that is incompatible with Brainapp's.
** Note that DTK (as of version 0.6.2.2 / 2012.09.20) puts some stupid restrictions on the input format for Q-ball reconstruction:
*** You must use .nii rather than .nii.gz files. This is because of a bug in the DTK GUI: it strips the .nii.gz extension for the internal representation of the input filename, but then adds a ".nii" when generating the command-line calls to its constituent tools. In this case, the process will fail on the second step (odf_recon). You can either run the command-line tools directly yourself, or use <code>gunzip</code> to fix this.
*** You must provide a set of sequentially-numbered 3D volumes (not a single 4-D volume with all of them concatenated). If you don't do this, DTK will give you an error complaining about "multiple high b values", even if your gradient table specifies only one. You can use <code>$G/common/mri/niftisplit</code> to get things the way it likes.

== See Also ==
* [[Diffusion Processing Pipeline/bugs and feature requests|Pipeline bugs and feature requests]]
* [[In-House Diffusion MRI Software]]

[[Category:Diffusion MRI]][[Category:Software]]

Neuroimaging Systems

2014-01-19T17:25:52Z

Jadrian Miles: /* Tools */ added link to a previous round-up of third-party tools

This page documents tools and projects related to software systems for dealing with neuroimaging data. The tools listed are some common visualization applications (some of which are general purpose). The projects listed either are generating a large amount of imaging data or developing systems to manage imaging data.

==Tools==
''See also [[3rd Party Diffusion MRI Software]].''

Volume Visualization
* [http://www.fmrib.ox.ac.uk/fsl/fslview/index.html FSLView]
* [http://www.mccauslandcenter.sc.edu/mricro/mricron/ MRIcron]
* [http://www-sop.inria.fr/asclepios/software/MedINRIA/ MedINRIA]

Shape Visualization
* [http://trackvis.org/ TrackVis]
* [http://www.loni.ucla.edu/Software/ShapeViewer ShapeViewer]
* [http://www.paraview.org/ Paraview]

Network Visualization
* [http://www.cytoscape.org/ Cytoscape]
* [http://gephi.org/ Gephi]
* [http://connectomeviewer.org/viewer/ ConnectomeViewer]

Challenges
* <i>Integration</i> of volume, geometry, network, tabular data
* <i>Query</i> by subject, metadata, anatomy, or statistics
* <i>Comparison</i> across subject, modalities, metrics
* <i>Coordinate systems</i>, including rigid, affine, non-linear
* <i>Memory</i> and <i>IO</i> bottlenecks

==Projects and Institutes==

* [http://ucnia.org/ University of Utah Center for Neuroimage Analysis]
* [http://www.humanconnectomeproject.org/ Human Connectome Project Harvard-UCLA-MGH]
* [http://www.neuroscienceblueprint.nih.gov/connectome/ Human Connectome WU-Minn]
* [http://www.mouseconnectome.org/ Mouse Connectome]
* [https://ida.loni.ucla.edu LONI Image Database Archive (IDA)]
* [http://www.ppmi-info.org/ Parkinson's Progression Marker's Initiative (PPMI)]
* [http://www.loni.ucla.edu/ICBM/ International Consortium of Brain Mapping (ICBM}]
* [http://adni.loni.ucla.edu/ Alzheimer's Disease Neuroimaging Initiative (ADNI)]
* [http://www.birncommunity.org/ Biomedical Informatics Research Network (BIRN)]
* [http://www.na-mic.org/ National Alliance for Medical Image Computing (NA-MIC)]
* [http://xnat.org/ Open Source Informatics for Biomedical Imaging Research (XNAT)]
* [https://cnda.wustl.edu/ Central Neuroimaging Data Archive]

Brain anatomy

2014-01-17T19:44:13Z

Jadrian Miles: /* Commissural Tracts */ cleaned up hippocampal commissure

This page is a dumping ground for anatomical terms that come up in conversation with neuroscientists, phrased (hopefully!) in a way that CS people can understand them and locate them in the brain. Click a tract name for more detailed information, including instructions for segmenting the tract out of a tractogram in [[Brainapp]].

If terms like "posterior", "inferior", and "sagittal" are confusing to you, check out the Wikipedia articles on [[w:Anatomical terms of location#Medical (human) directional terms|anatomical directions]] and [[w:Anatomical terms of location#Planes|anatomical planes]].

== Types of Tissue ==
The tissue of the nervous system may be grossly divided into two types: '''grey matter''' and '''white matter'''. In the grey matter, neuron bodies are packed relatively closely together, while the white matter is made up mostly of neuronal projections, called ''axons''. The outer surfaces of the brain as well as a few internal structures are composed of grey matter, while much of the interior of the brain is composed of white matter. Bundles of axons in the white matter are called '''tracts''' and connect different grey matter regions together.

== Parts of the Brain ==
The following diagram shows the lobes of the cerebrum, the outer structures of the forebrain.

[[Image:Gray728.svg|thumb|300px|center|Lobes and major fissures of the cerebrum, in a lateral view.]]

The structure inferior to the temporal lobe and posterior to the spinal cord is the '''cerebellum'''.

The outer grey matter layer of the brain is called the '''cortex'''.

== White Matter Tracts ==
<center>
<gallery widths="300px" heights="250px">
Image:Brain sagittal section.jpg|A sagittal section of a human brain. Click this image for a high-res version in which you can read the annotations.
Image:Gray751.png|Major association fibers in the cerebrum, in a mid-sagittal lateral view.
</gallery>
</center>

There are three major types of tracts in the brain:
* '''[[w:Commissural fibers|Commissural fibers]]''' or '''transverse fibers''' connect equivalent grey matter sites in the two hemispheres of the brain.
* '''[[w:Association fiber|Association fibers]]''' connect different cortical grey matter sites to each other.
* '''[[w:Projection fibers|Projection fibers]]''' connect cortical sites to subcortical grey matter or to the spinal cord.

=== Commissural Tracts ===
The vast majority of commissural tracts cross between the hemispheres in a single localized region called the corpus callosum. Strictly speaking, the corpus callosum is not itself a tract, because it describes only the medial portion of each tract.

; Corpus callosum (CC)
: The large, central collection of left-right-running fibers connecting the hemispheres. In a mid-sagittal cutting plane, it looks like a letter C turned on its side, with the tips pointing inferior (and the fibers running orthogonal to the plane); see the illustration above, or [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p8.html]. Though the distal portions of the fibers that make up the CC are grouped into separate tracts in the interior of each hemisphere, they are collectively called the CC where they cross the mid-sagittal plane. In this sense the CC is more of a place name than a tract name; it indicates only the portions of those fibers that are near the mid-sagittal plane. Moving around the CC from the back (posterior), it is subdivided into parts named:
:; Splenium
:: The posterior, slightly bulbous part of the CC.
:; Body
:: The more-or-less flat part of the CC between the splenium and the genu.
:; Genu
:: The anterior part of the CC, where it bends back on itself. "Genu" means "knee".
:; Rostrum
:: The part of the CC inferior and posterior to the genu.
: The fibers that make up the corpus callosum may be grouped into entire tracts, and identified both by their structure and by the region of the CC through which they pass:
:; Forceps major / forceps posterior
:: The posterior projection of the CC (from the splenium) into the occipital lobe (the back of the brain). In an axial section, it looks like a letter C at the posterior portion of the brain with the tips pointing posterior. See [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p7.html].
:; Forceps minor / forceps anterior
:: The anterior projection of the CC (from the genu) into the cerebrum (the front of the brain). In an axial section, it looks like a letter C at the anterior portion of the brain with the tips pointing anterior. In other words, it looks sort of like a pair of mandibles over the eyes. See [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p7.html].
:; Tapetum
:: A medial projection of the CC (from the body) into the temporal lobe. In a well-reconstructed 3D tractogram, it forms a small horizontal fanning sheet of fibers emanating from the CC.
: (Note that the list above is not exhaustive—there are other named tracts that pass through the CC too.)

; Anterior commissure
: A smaller band of fibers that crosses between the hemispheres inferior to the CC.
; Posterior commissure
: Another smaller band of commissural fibers inferior to the CC and posterior to the anterior commissure.
; Hippocampal commissure (or lyra, or commissue of the fornix)
: A very small, sheet-shaped band of fibers connecting the two hippocampi. These connect to, and join the fibers of, the fornix in either hemisphere.

=== Association Tracts ===
; [[/Cingulum bundle|Cingulum / cingulum bundle]]
: White matter fibers located just superior to the corpus callosum, but running anterior-posterior. In a para-sagittal section, they look like a letter C turned on its side, with the tips pointing inferior, stacked right on top of the CC. In a coronal section, they look like two small circles just superior to the CC on either side of the interhemispheric fissure, with fibers running orthogonal to the plane.
; Fornix
: C-shaped pathways that surrounds the subcortical gray matter in each hemisphere. It connects the hippocampus to the hypothalamus. Difficult to track due its curvature and partial voluming with gray matter.
; Inferior longitudinal fasciculus (ILF)
: A pathway that runs from the occipital to temporal cortices in each hemisphere. The majority of the fibers are in the temporal lobe.
; Superior longitudinal fasciculus (SLF)
: A collection of pathways that run between the frontal lobe and the temporal, parietal, and occipital lobes in each hemisphere. There are several subdivisions typically made based on their posterior connections.
:; SLF I
:: The portion of the SLF that intersects the corpus callosum and connects superior frontal cortex to parietal and occipital cortex. Typically not reconstructed with the single tensor model.
:; SLF II
:: The portion of the SLF that connects lateral frontal white matter (such as DLPFC) to the parietal and occipital cortices. Sometimes reconstructed with single tensors.
:; SLF III
:: The portion superior to the arcuate that connects lateral-inferior frontal cortex to parietal cortex. These fibers are very similar to the arcuate but do not curve.
:; Arcuate fasciculus (AF)
:: The portion of the SLF that curves to connect frontal cortex to the temporal lobe.
; Uncinate fasciculus
: A pathway that connects inferior frontal cortex to the temporal pole in each hemisphere. This curves around the insula cortex. Sometimes difficult to track due to high curvature.

=== Projection Tracts ===
; Corona radiata
: A fan-shaped sheet of WM that radiates superior (upward) from the brain stem to the cortex in each hemisphere. The fibers of the corona radiata run superior-inferior, and the fanning is anterior-posterior. The sheet is flat and thin in the left-right dimension; its orientation is approximated by a sagittal cutting plane.
; [[/Corticospinal tract|Corticospinal tract]] (CST)
: A major descending pathway that projects from the cerebral cortex to the spinal cord. It is the key pathway for voluntary movement (contrast it with the other major longitudinal but ascending pathway: the dorsal-column medial lemniscal system). Also, this is a good point to remember that tracts are generally named in source-to-target fashion. For example, corticospinal tract originates from the cortex and projects to the spinal cord, similarly corticobulbar tract goes from the cortex to the bulbar (well, brain stem), etc.
; Internal capsule
: White matter structure that runs between the cortex and medulla, containing major longitudinal (both ascending and descending) pathway systems, including the corticospinal tract, dorsal column medial lemniscus (DCML) system (only medial lemniscus part), corticobulbar tract, etc.

== Grey Matter Structures ==
; Thalamus
: Major relay nuclei (grey matter structures) in the diencephalon (division of the brain primarily containing thalamus and hypothalamus in mature brain). Most sensory information is carried to the thalamus first (i.e., via ascending tracts) and then relayed to the cerebral cortex. Similarly, neural signals controlling movements, learning, memory and emotions bound to sub-cortical structures are relayed by the thalamus to their final destinations.
; [[w:Hippocampus|Hippocampus]]
: Paired horn-shaped structures beneath the medial surface of the temporal lobes. Each half of the hippocampus is an elaboration of the edge of the cerebral cortex, where it folds up and inward from the inferior surface of the temporal lobe and curls around on itself. The hippocampus is associated with spatial memory.

== External Links ==
* [http://www.brainnav.com BrainNavigator] --- an interactive 3D atlas application with labeled brain structures and histology thumbnails for rat and mouse brains. Does not include WM structures.
* [http://braininfo.rprc.washington.edu BrainInfo] --- an interactive visual and textual guide to thousands of named anatomical structures of the macaque brain. Includes WM ''regions'' (e.g. "inferior temporal white matter") but not fascicles ("superior longitudinal fasciculus").
* [http://brainmaps.org BrainMaps.org] --- a database of histology of brains from various species, with an interactive online viewer
* [http://www.asnr2.org/neurographics/7/1/26/White%20Matter%20Tract%20Anatomy/DTI%20tutorial%201.html WM Anatomy Tutorial with DTI pictures]
* [http://www.biology-online.org/dictionary Biology-Online dictionary] --- search for text descriptions of terms
* [http://anatomy.uams.edu/anatomyhtml/neuro_atlas.html U. Arkansas neuroanatomy atlas images]
* [http://radiopaedia.org/encyclopaedia/anatomy/central-nervous-system Radiopaedia] --- a wiki encyclopedia for radiology; search for articles
* [http://www.bartleby.com/107/index.html#chap10 Gray's Anatomy] --- an illustrated anatomy textbook from 1918
* [https://www.mristudio.org MRI Studio] is a program that supposedly includes [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2478641 Mori, et al.'s 2008 multi-subject DTI-based WM atlas]

[[Category:Diffusion MRI]]

Brain anatomy

2014-01-17T19:41:28Z

Jadrian Miles: /* Association Tracts */ clarified orientation of cingulum

This page is a dumping ground for anatomical terms that come up in conversation with neuroscientists, phrased (hopefully!) in a way that CS people can understand them and locate them in the brain. Click a tract name for more detailed information, including instructions for segmenting the tract out of a tractogram in [[Brainapp]].

If terms like "posterior", "inferior", and "sagittal" are confusing to you, check out the Wikipedia articles on [[w:Anatomical terms of location#Medical (human) directional terms|anatomical directions]] and [[w:Anatomical terms of location#Planes|anatomical planes]].

== Types of Tissue ==
The tissue of the nervous system may be grossly divided into two types: '''grey matter''' and '''white matter'''. In the grey matter, neuron bodies are packed relatively closely together, while the white matter is made up mostly of neuronal projections, called ''axons''. The outer surfaces of the brain as well as a few internal structures are composed of grey matter, while much of the interior of the brain is composed of white matter. Bundles of axons in the white matter are called '''tracts''' and connect different grey matter regions together.

== Parts of the Brain ==
The following diagram shows the lobes of the cerebrum, the outer structures of the forebrain.

[[Image:Gray728.svg|thumb|300px|center|Lobes and major fissures of the cerebrum, in a lateral view.]]

The structure inferior to the temporal lobe and posterior to the spinal cord is the '''cerebellum'''.

The outer grey matter layer of the brain is called the '''cortex'''.

== White Matter Tracts ==
<center>
<gallery widths="300px" heights="250px">
Image:Brain sagittal section.jpg|A sagittal section of a human brain. Click this image for a high-res version in which you can read the annotations.
Image:Gray751.png|Major association fibers in the cerebrum, in a mid-sagittal lateral view.
</gallery>
</center>

There are three major types of tracts in the brain:
* '''[[w:Commissural fibers|Commissural fibers]]''' or '''transverse fibers''' connect equivalent grey matter sites in the two hemispheres of the brain.
* '''[[w:Association fiber|Association fibers]]''' connect different cortical grey matter sites to each other.
* '''[[w:Projection fibers|Projection fibers]]''' connect cortical sites to subcortical grey matter or to the spinal cord.

=== Commissural Tracts ===
The vast majority of commissural tracts cross between the hemispheres in a single localized region called the corpus callosum. Strictly speaking, the corpus callosum is not itself a tract, because it describes only the medial portion of each tract.

; Corpus callosum (CC)
: The large, central collection of left-right-running fibers connecting the hemispheres. In a mid-sagittal cutting plane, it looks like a letter C turned on its side, with the tips pointing inferior (and the fibers running orthogonal to the plane); see the illustration above, or [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p8.html]. Though the distal portions of the fibers that make up the CC are grouped into separate tracts in the interior of each hemisphere, they are collectively called the CC where they cross the mid-sagittal plane. In this sense the CC is more of a place name than a tract name; it indicates only the portions of those fibers that are near the mid-sagittal plane. Moving around the CC from the back (posterior), it is subdivided into parts named:
:; Splenium
:: The posterior, slightly bulbous part of the CC.
:; Body
:: The more-or-less flat part of the CC between the splenium and the genu.
:; Genu
:: The anterior part of the CC, where it bends back on itself. "Genu" means "knee".
:; Rostrum
:: The part of the CC inferior and posterior to the genu.
: The fibers that make up the corpus callosum may be grouped into entire tracts, and identified both by their structure and by the region of the CC through which they pass:
:; Forceps major / forceps posterior
:: The posterior projection of the CC (from the splenium) into the occipital lobe (the back of the brain). In an axial section, it looks like a letter C at the posterior portion of the brain with the tips pointing posterior. See [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p7.html].
:; Forceps minor / forceps anterior
:: The anterior projection of the CC (from the genu) into the cerebrum (the front of the brain). In an axial section, it looks like a letter C at the anterior portion of the brain with the tips pointing anterior. In other words, it looks sort of like a pair of mandibles over the eyes. See [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p7.html].
:; Tapetum
:: A medial projection of the CC (from the body) into the temporal lobe. In a well-reconstructed 3D tractogram, it forms a small horizontal fanning sheet of fibers emanating from the CC.
: (Note that the list above is not exhaustive—there are other named tracts that pass through the CC too.)

; Anterior commissure
: A smaller band of fibers that crosses between the hemispheres inferior to the CC.
; Posterior commissure
: Another smaller band of commissural fibers inferior to the CC and posterior to the anterior commissure.
; Hippocampal commissure (or lyra, or commissue of the fornix)
: A very small, sheet-shaped band of fibers connecting the two halves (hippocampi) of the fornix.

=== Association Tracts ===
; [[/Cingulum bundle|Cingulum / cingulum bundle]]
: White matter fibers located just superior to the corpus callosum, but running anterior-posterior. In a para-sagittal section, they look like a letter C turned on its side, with the tips pointing inferior, stacked right on top of the CC. In a coronal section, they look like two small circles just superior to the CC on either side of the interhemispheric fissure, with fibers running orthogonal to the plane.
; Fornix
: C-shaped pathways that surrounds the subcortical gray matter in each hemisphere. It connects the hippocampus to the hypothalamus. Difficult to track due its curvature and partial voluming with gray matter.
; Inferior longitudinal fasciculus (ILF)
: A pathway that runs from the occipital to temporal cortices in each hemisphere. The majority of the fibers are in the temporal lobe.
; Superior longitudinal fasciculus (SLF)
: A collection of pathways that run between the frontal lobe and the temporal, parietal, and occipital lobes in each hemisphere. There are several subdivisions typically made based on their posterior connections.
:; SLF I
:: The portion of the SLF that intersects the corpus callosum and connects superior frontal cortex to parietal and occipital cortex. Typically not reconstructed with the single tensor model.
:; SLF II
:: The portion of the SLF that connects lateral frontal white matter (such as DLPFC) to the parietal and occipital cortices. Sometimes reconstructed with single tensors.
:; SLF III
:: The portion superior to the arcuate that connects lateral-inferior frontal cortex to parietal cortex. These fibers are very similar to the arcuate but do not curve.
:; Arcuate fasciculus (AF)
:: The portion of the SLF that curves to connect frontal cortex to the temporal lobe.
; Uncinate fasciculus
: A pathway that connects inferior frontal cortex to the temporal pole in each hemisphere. This curves around the insula cortex. Sometimes difficult to track due to high curvature.

=== Projection Tracts ===
; Corona radiata
: A fan-shaped sheet of WM that radiates superior (upward) from the brain stem to the cortex in each hemisphere. The fibers of the corona radiata run superior-inferior, and the fanning is anterior-posterior. The sheet is flat and thin in the left-right dimension; its orientation is approximated by a sagittal cutting plane.
; [[/Corticospinal tract|Corticospinal tract]] (CST)
: A major descending pathway that projects from the cerebral cortex to the spinal cord. It is the key pathway for voluntary movement (contrast it with the other major longitudinal but ascending pathway: the dorsal-column medial lemniscal system). Also, this is a good point to remember that tracts are generally named in source-to-target fashion. For example, corticospinal tract originates from the cortex and projects to the spinal cord, similarly corticobulbar tract goes from the cortex to the bulbar (well, brain stem), etc.
; Internal capsule
: White matter structure that runs between the cortex and medulla, containing major longitudinal (both ascending and descending) pathway systems, including the corticospinal tract, dorsal column medial lemniscus (DCML) system (only medial lemniscus part), corticobulbar tract, etc.

== Grey Matter Structures ==
; Thalamus
: Major relay nuclei (grey matter structures) in the diencephalon (division of the brain primarily containing thalamus and hypothalamus in mature brain). Most sensory information is carried to the thalamus first (i.e., via ascending tracts) and then relayed to the cerebral cortex. Similarly, neural signals controlling movements, learning, memory and emotions bound to sub-cortical structures are relayed by the thalamus to their final destinations.
; [[w:Hippocampus|Hippocampus]]
: Paired horn-shaped structures beneath the medial surface of the temporal lobes. Each half of the hippocampus is an elaboration of the edge of the cerebral cortex, where it folds up and inward from the inferior surface of the temporal lobe and curls around on itself. The hippocampus is associated with spatial memory.

== External Links ==
* [http://www.brainnav.com BrainNavigator] --- an interactive 3D atlas application with labeled brain structures and histology thumbnails for rat and mouse brains. Does not include WM structures.
* [http://braininfo.rprc.washington.edu BrainInfo] --- an interactive visual and textual guide to thousands of named anatomical structures of the macaque brain. Includes WM ''regions'' (e.g. "inferior temporal white matter") but not fascicles ("superior longitudinal fasciculus").
* [http://brainmaps.org BrainMaps.org] --- a database of histology of brains from various species, with an interactive online viewer
* [http://www.asnr2.org/neurographics/7/1/26/White%20Matter%20Tract%20Anatomy/DTI%20tutorial%201.html WM Anatomy Tutorial with DTI pictures]
* [http://www.biology-online.org/dictionary Biology-Online dictionary] --- search for text descriptions of terms
* [http://anatomy.uams.edu/anatomyhtml/neuro_atlas.html U. Arkansas neuroanatomy atlas images]
* [http://radiopaedia.org/encyclopaedia/anatomy/central-nervous-system Radiopaedia] --- a wiki encyclopedia for radiology; search for articles
* [http://www.bartleby.com/107/index.html#chap10 Gray's Anatomy] --- an illustrated anatomy textbook from 1918
* [https://www.mristudio.org MRI Studio] is a program that supposedly includes [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2478641 Mori, et al.'s 2008 multi-subject DTI-based WM atlas]

[[Category:Diffusion MRI]]

Brain anatomy

2014-01-17T19:40:35Z

Jadrian Miles: /* Commissural Tracts */ added the other small commissural tracts

This page is a dumping ground for anatomical terms that come up in conversation with neuroscientists, phrased (hopefully!) in a way that CS people can understand them and locate them in the brain. Click a tract name for more detailed information, including instructions for segmenting the tract out of a tractogram in [[Brainapp]].

If terms like "posterior", "inferior", and "sagittal" are confusing to you, check out the Wikipedia articles on [[w:Anatomical terms of location#Medical (human) directional terms|anatomical directions]] and [[w:Anatomical terms of location#Planes|anatomical planes]].

== Types of Tissue ==
The tissue of the nervous system may be grossly divided into two types: '''grey matter''' and '''white matter'''. In the grey matter, neuron bodies are packed relatively closely together, while the white matter is made up mostly of neuronal projections, called ''axons''. The outer surfaces of the brain as well as a few internal structures are composed of grey matter, while much of the interior of the brain is composed of white matter. Bundles of axons in the white matter are called '''tracts''' and connect different grey matter regions together.

== Parts of the Brain ==
The following diagram shows the lobes of the cerebrum, the outer structures of the forebrain.

[[Image:Gray728.svg|thumb|300px|center|Lobes and major fissures of the cerebrum, in a lateral view.]]

The structure inferior to the temporal lobe and posterior to the spinal cord is the '''cerebellum'''.

The outer grey matter layer of the brain is called the '''cortex'''.

== White Matter Tracts ==
<center>
<gallery widths="300px" heights="250px">
Image:Brain sagittal section.jpg|A sagittal section of a human brain. Click this image for a high-res version in which you can read the annotations.
Image:Gray751.png|Major association fibers in the cerebrum, in a mid-sagittal lateral view.
</gallery>
</center>

There are three major types of tracts in the brain:
* '''[[w:Commissural fibers|Commissural fibers]]''' or '''transverse fibers''' connect equivalent grey matter sites in the two hemispheres of the brain.
* '''[[w:Association fiber|Association fibers]]''' connect different cortical grey matter sites to each other.
* '''[[w:Projection fibers|Projection fibers]]''' connect cortical sites to subcortical grey matter or to the spinal cord.

=== Commissural Tracts ===
The vast majority of commissural tracts cross between the hemispheres in a single localized region called the corpus callosum. Strictly speaking, the corpus callosum is not itself a tract, because it describes only the medial portion of each tract.

; Corpus callosum (CC)
: The large, central collection of left-right-running fibers connecting the hemispheres. In a mid-sagittal cutting plane, it looks like a letter C turned on its side, with the tips pointing inferior (and the fibers running orthogonal to the plane); see the illustration above, or [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p8.html]. Though the distal portions of the fibers that make up the CC are grouped into separate tracts in the interior of each hemisphere, they are collectively called the CC where they cross the mid-sagittal plane. In this sense the CC is more of a place name than a tract name; it indicates only the portions of those fibers that are near the mid-sagittal plane. Moving around the CC from the back (posterior), it is subdivided into parts named:
:; Splenium
:: The posterior, slightly bulbous part of the CC.
:; Body
:: The more-or-less flat part of the CC between the splenium and the genu.
:; Genu
:: The anterior part of the CC, where it bends back on itself. "Genu" means "knee".
:; Rostrum
:: The part of the CC inferior and posterior to the genu.
: The fibers that make up the corpus callosum may be grouped into entire tracts, and identified both by their structure and by the region of the CC through which they pass:
:; Forceps major / forceps posterior
:: The posterior projection of the CC (from the splenium) into the occipital lobe (the back of the brain). In an axial section, it looks like a letter C at the posterior portion of the brain with the tips pointing posterior. See [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p7.html].
:; Forceps minor / forceps anterior
:: The anterior projection of the CC (from the genu) into the cerebrum (the front of the brain). In an axial section, it looks like a letter C at the anterior portion of the brain with the tips pointing anterior. In other words, it looks sort of like a pair of mandibles over the eyes. See [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p7.html].
:; Tapetum
:: A medial projection of the CC (from the body) into the temporal lobe. In a well-reconstructed 3D tractogram, it forms a small horizontal fanning sheet of fibers emanating from the CC.
: (Note that the list above is not exhaustive—there are other named tracts that pass through the CC too.)

; Anterior commissure
: A smaller band of fibers that crosses between the hemispheres inferior to the CC.
; Posterior commissure
: Another smaller band of commissural fibers inferior to the CC and posterior to the anterior commissure.
; Hippocampal commissure (or lyra, or commissue of the fornix)
: A very small, sheet-shaped band of fibers connecting the two halves (hippocampi) of the fornix.

=== Association Tracts ===
; [[/Cingulum bundle|Cingulum / cingulum bundle]]
: White matter fibers located just superior to the corpus callosum, but running anterior-posterior. In a para-sagittal section, they look like a letter C turned on its side, with the tips pointing inferior, stacked right on top of the CC. In a coronal section, they look like two small circles just superior to the CC on either side of the interhemispheric fissure.
; Fornix
: C-shaped pathways that surrounds the subcortical gray matter in each hemisphere. It connects the hippocampus to the hypothalamus. Difficult to track due its curvature and partial voluming with gray matter.
; Inferior longitudinal fasciculus (ILF)
: A pathway that runs from the occipital to temporal cortices in each hemisphere. The majority of the fibers are in the temporal lobe.
; Superior longitudinal fasciculus (SLF)
: A collection of pathways that run between the frontal lobe and the temporal, parietal, and occipital lobes in each hemisphere. There are several subdivisions typically made based on their posterior connections.
:; SLF I
:: The portion of the SLF that intersects the corpus callosum and connects superior frontal cortex to parietal and occipital cortex. Typically not reconstructed with the single tensor model.
:; SLF II
:: The portion of the SLF that connects lateral frontal white matter (such as DLPFC) to the parietal and occipital cortices. Sometimes reconstructed with single tensors.
:; SLF III
:: The portion superior to the arcuate that connects lateral-inferior frontal cortex to parietal cortex. These fibers are very similar to the arcuate but do not curve.
:; Arcuate fasciculus (AF)
:: The portion of the SLF that curves to connect frontal cortex to the temporal lobe.
; Uncinate fasciculus
: A pathway that connects inferior frontal cortex to the temporal pole in each hemisphere. This curves around the insula cortex. Sometimes difficult to track due to high curvature.

=== Projection Tracts ===
; Corona radiata
: A fan-shaped sheet of WM that radiates superior (upward) from the brain stem to the cortex in each hemisphere. The fibers of the corona radiata run superior-inferior, and the fanning is anterior-posterior. The sheet is flat and thin in the left-right dimension; its orientation is approximated by a sagittal cutting plane.
; [[/Corticospinal tract|Corticospinal tract]] (CST)
: A major descending pathway that projects from the cerebral cortex to the spinal cord. It is the key pathway for voluntary movement (contrast it with the other major longitudinal but ascending pathway: the dorsal-column medial lemniscal system). Also, this is a good point to remember that tracts are generally named in source-to-target fashion. For example, corticospinal tract originates from the cortex and projects to the spinal cord, similarly corticobulbar tract goes from the cortex to the bulbar (well, brain stem), etc.
; Internal capsule
: White matter structure that runs between the cortex and medulla, containing major longitudinal (both ascending and descending) pathway systems, including the corticospinal tract, dorsal column medial lemniscus (DCML) system (only medial lemniscus part), corticobulbar tract, etc.

== Grey Matter Structures ==
; Thalamus
: Major relay nuclei (grey matter structures) in the diencephalon (division of the brain primarily containing thalamus and hypothalamus in mature brain). Most sensory information is carried to the thalamus first (i.e., via ascending tracts) and then relayed to the cerebral cortex. Similarly, neural signals controlling movements, learning, memory and emotions bound to sub-cortical structures are relayed by the thalamus to their final destinations.
; [[w:Hippocampus|Hippocampus]]
: Paired horn-shaped structures beneath the medial surface of the temporal lobes. Each half of the hippocampus is an elaboration of the edge of the cerebral cortex, where it folds up and inward from the inferior surface of the temporal lobe and curls around on itself. The hippocampus is associated with spatial memory.

== External Links ==
* [http://www.brainnav.com BrainNavigator] --- an interactive 3D atlas application with labeled brain structures and histology thumbnails for rat and mouse brains. Does not include WM structures.
* [http://braininfo.rprc.washington.edu BrainInfo] --- an interactive visual and textual guide to thousands of named anatomical structures of the macaque brain. Includes WM ''regions'' (e.g. "inferior temporal white matter") but not fascicles ("superior longitudinal fasciculus").
* [http://brainmaps.org BrainMaps.org] --- a database of histology of brains from various species, with an interactive online viewer
* [http://www.asnr2.org/neurographics/7/1/26/White%20Matter%20Tract%20Anatomy/DTI%20tutorial%201.html WM Anatomy Tutorial with DTI pictures]
* [http://www.biology-online.org/dictionary Biology-Online dictionary] --- search for text descriptions of terms
* [http://anatomy.uams.edu/anatomyhtml/neuro_atlas.html U. Arkansas neuroanatomy atlas images]
* [http://radiopaedia.org/encyclopaedia/anatomy/central-nervous-system Radiopaedia] --- a wiki encyclopedia for radiology; search for articles
* [http://www.bartleby.com/107/index.html#chap10 Gray's Anatomy] --- an illustrated anatomy textbook from 1918
* [https://www.mristudio.org MRI Studio] is a program that supposedly includes [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2478641 Mori, et al.'s 2008 multi-subject DTI-based WM atlas]

[[Category:Diffusion MRI]]

Brain anatomy

2014-01-17T19:36:32Z

Jadrian Miles: /* Commissural Tracts */ clarified about the CC

This page is a dumping ground for anatomical terms that come up in conversation with neuroscientists, phrased (hopefully!) in a way that CS people can understand them and locate them in the brain. Click a tract name for more detailed information, including instructions for segmenting the tract out of a tractogram in [[Brainapp]].

If terms like "posterior", "inferior", and "sagittal" are confusing to you, check out the Wikipedia articles on [[w:Anatomical terms of location#Medical (human) directional terms|anatomical directions]] and [[w:Anatomical terms of location#Planes|anatomical planes]].

== Types of Tissue ==
The tissue of the nervous system may be grossly divided into two types: '''grey matter''' and '''white matter'''. In the grey matter, neuron bodies are packed relatively closely together, while the white matter is made up mostly of neuronal projections, called ''axons''. The outer surfaces of the brain as well as a few internal structures are composed of grey matter, while much of the interior of the brain is composed of white matter. Bundles of axons in the white matter are called '''tracts''' and connect different grey matter regions together.

== Parts of the Brain ==
The following diagram shows the lobes of the cerebrum, the outer structures of the forebrain.

[[Image:Gray728.svg|thumb|300px|center|Lobes and major fissures of the cerebrum, in a lateral view.]]

The structure inferior to the temporal lobe and posterior to the spinal cord is the '''cerebellum'''.

The outer grey matter layer of the brain is called the '''cortex'''.

== White Matter Tracts ==
<center>
<gallery widths="300px" heights="250px">
Image:Brain sagittal section.jpg|A sagittal section of a human brain. Click this image for a high-res version in which you can read the annotations.
Image:Gray751.png|Major association fibers in the cerebrum, in a mid-sagittal lateral view.
</gallery>
</center>

There are three major types of tracts in the brain:
* '''[[w:Commissural fibers|Commissural fibers]]''' or '''transverse fibers''' connect equivalent grey matter sites in the two hemispheres of the brain.
* '''[[w:Association fiber|Association fibers]]''' connect different cortical grey matter sites to each other.
* '''[[w:Projection fibers|Projection fibers]]''' connect cortical sites to subcortical grey matter or to the spinal cord.

=== Commissural Tracts ===
The vast majority of commissural tracts cross between the hemispheres in a single localized region called the corpus callosum. Strictly speaking, the corpus callosum is not itself a tract, because it describes only the medial portion of each tract.

; Corpus callosum (CC)
: The large, central collection of left-right-running fibers connecting the hemispheres. In a mid-sagittal cutting plane, it looks like a letter C turned on its side, with the tips pointing inferior (and the fibers running orthogonal to the plane); see the illustration above, or [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p8.html]. Though the distal portions of the fibers that make up the CC are grouped into separate tracts in the interior of each hemisphere, they are collectively called the CC where they cross the mid-sagittal plane. In this sense the CC is more of a place name than a tract name; it indicates only the portions of those fibers that are near the mid-sagittal plane. Moving around the CC from the back (posterior), it is subdivided into parts named:
:; Splenium
:: The posterior, slightly bulbous part of the CC.
:; Body
:: The more-or-less flat part of the CC between the splenium and the genu.
:; Genu
:: The anterior part of the CC, where it bends back on itself. "Genu" means "knee".
:; Rostrum
:: The part of the CC inferior and posterior to the genu.
: The fibers that make up the corpus callosum may be grouped into entire tracts, and identified both by their structure and by the region of the CC through which they pass:
:; Forceps major / forceps posterior
:: The posterior projection of the CC (from the splenium) into the occipital lobe (the back of the brain). In an axial section, it looks like a letter C at the posterior portion of the brain with the tips pointing posterior. See [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p7.html].
:; Forceps minor / forceps anterior
:: The anterior projection of the CC (from the genu) into the cerebrum (the front of the brain). In an axial section, it looks like a letter C at the anterior portion of the brain with the tips pointing anterior. In other words, it looks sort of like a pair of mandibles over the eyes. See [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p7.html].
:; Tapetum
:: A medial projection of the CC (from the body) into the temporal lobe. In a well-reconstructed 3D tractogram, it forms a small horizontal fanning sheet of fibers emanating from the CC.
: (Note that the list above is not exhaustive—there are other named tracts that pass through the CC too.)

=== Association Tracts ===
; [[/Cingulum bundle|Cingulum / cingulum bundle]]
: White matter fibers located just superior to the corpus callosum, but running anterior-posterior. In a para-sagittal section, they look like a letter C turned on its side, with the tips pointing inferior, stacked right on top of the CC. In a coronal section, they look like two small circles just superior to the CC on either side of the interhemispheric fissure.
; Fornix
: C-shaped pathways that surrounds the subcortical gray matter in each hemisphere. It connects the hippocampus to the hypothalamus. Difficult to track due its curvature and partial voluming with gray matter.
; Inferior longitudinal fasciculus (ILF)
: A pathway that runs from the occipital to temporal cortices in each hemisphere. The majority of the fibers are in the temporal lobe.
; Superior longitudinal fasciculus (SLF)
: A collection of pathways that run between the frontal lobe and the temporal, parietal, and occipital lobes in each hemisphere. There are several subdivisions typically made based on their posterior connections.
:; SLF I
:: The portion of the SLF that intersects the corpus callosum and connects superior frontal cortex to parietal and occipital cortex. Typically not reconstructed with the single tensor model.
:; SLF II
:: The portion of the SLF that connects lateral frontal white matter (such as DLPFC) to the parietal and occipital cortices. Sometimes reconstructed with single tensors.
:; SLF III
:: The portion superior to the arcuate that connects lateral-inferior frontal cortex to parietal cortex. These fibers are very similar to the arcuate but do not curve.
:; Arcuate fasciculus (AF)
:: The portion of the SLF that curves to connect frontal cortex to the temporal lobe.
; Uncinate fasciculus
: A pathway that connects inferior frontal cortex to the temporal pole in each hemisphere. This curves around the insula cortex. Sometimes difficult to track due to high curvature.

=== Projection Tracts ===
; Corona radiata
: A fan-shaped sheet of WM that radiates superior (upward) from the brain stem to the cortex in each hemisphere. The fibers of the corona radiata run superior-inferior, and the fanning is anterior-posterior. The sheet is flat and thin in the left-right dimension; its orientation is approximated by a sagittal cutting plane.
; [[/Corticospinal tract|Corticospinal tract]] (CST)
: A major descending pathway that projects from the cerebral cortex to the spinal cord. It is the key pathway for voluntary movement (contrast it with the other major longitudinal but ascending pathway: the dorsal-column medial lemniscal system). Also, this is a good point to remember that tracts are generally named in source-to-target fashion. For example, corticospinal tract originates from the cortex and projects to the spinal cord, similarly corticobulbar tract goes from the cortex to the bulbar (well, brain stem), etc.
; Internal capsule
: White matter structure that runs between the cortex and medulla, containing major longitudinal (both ascending and descending) pathway systems, including the corticospinal tract, dorsal column medial lemniscus (DCML) system (only medial lemniscus part), corticobulbar tract, etc.

== Grey Matter Structures ==
; Thalamus
: Major relay nuclei (grey matter structures) in the diencephalon (division of the brain primarily containing thalamus and hypothalamus in mature brain). Most sensory information is carried to the thalamus first (i.e., via ascending tracts) and then relayed to the cerebral cortex. Similarly, neural signals controlling movements, learning, memory and emotions bound to sub-cortical structures are relayed by the thalamus to their final destinations.
; [[w:Hippocampus|Hippocampus]]
: Paired horn-shaped structures beneath the medial surface of the temporal lobes. Each half of the hippocampus is an elaboration of the edge of the cerebral cortex, where it folds up and inward from the inferior surface of the temporal lobe and curls around on itself. The hippocampus is associated with spatial memory.

== External Links ==
* [http://www.brainnav.com BrainNavigator] --- an interactive 3D atlas application with labeled brain structures and histology thumbnails for rat and mouse brains. Does not include WM structures.
* [http://braininfo.rprc.washington.edu BrainInfo] --- an interactive visual and textual guide to thousands of named anatomical structures of the macaque brain. Includes WM ''regions'' (e.g. "inferior temporal white matter") but not fascicles ("superior longitudinal fasciculus").
* [http://brainmaps.org BrainMaps.org] --- a database of histology of brains from various species, with an interactive online viewer
* [http://www.asnr2.org/neurographics/7/1/26/White%20Matter%20Tract%20Anatomy/DTI%20tutorial%201.html WM Anatomy Tutorial with DTI pictures]
* [http://www.biology-online.org/dictionary Biology-Online dictionary] --- search for text descriptions of terms
* [http://anatomy.uams.edu/anatomyhtml/neuro_atlas.html U. Arkansas neuroanatomy atlas images]
* [http://radiopaedia.org/encyclopaedia/anatomy/central-nervous-system Radiopaedia] --- a wiki encyclopedia for radiology; search for articles
* [http://www.bartleby.com/107/index.html#chap10 Gray's Anatomy] --- an illustrated anatomy textbook from 1918
* [https://www.mristudio.org MRI Studio] is a program that supposedly includes [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2478641 Mori, et al.'s 2008 multi-subject DTI-based WM atlas]

[[Category:Diffusion MRI]]

Brain anatomy

2014-01-17T19:24:43Z

Jadrian Miles: /* Commissural Tracts */ removed dead link to illustration of commissural fibers

This page is a dumping ground for anatomical terms that come up in conversation with neuroscientists, phrased (hopefully!) in a way that CS people can understand them and locate them in the brain. Click a tract name for more detailed information, including instructions for segmenting the tract out of a tractogram in [[Brainapp]].

If terms like "posterior", "inferior", and "sagittal" are confusing to you, check out the Wikipedia articles on [[w:Anatomical terms of location#Medical (human) directional terms|anatomical directions]] and [[w:Anatomical terms of location#Planes|anatomical planes]].

== Types of Tissue ==
The tissue of the nervous system may be grossly divided into two types: '''grey matter''' and '''white matter'''. In the grey matter, neuron bodies are packed relatively closely together, while the white matter is made up mostly of neuronal projections, called ''axons''. The outer surfaces of the brain as well as a few internal structures are composed of grey matter, while much of the interior of the brain is composed of white matter. Bundles of axons in the white matter are called '''tracts''' and connect different grey matter regions together.

== Parts of the Brain ==
The following diagram shows the lobes of the cerebrum, the outer structures of the forebrain.

[[Image:Gray728.svg|thumb|300px|center|Lobes and major fissures of the cerebrum, in a lateral view.]]

The structure inferior to the temporal lobe and posterior to the spinal cord is the '''cerebellum'''.

The outer grey matter layer of the brain is called the '''cortex'''.

== White Matter Tracts ==
<center>
<gallery widths="300px" heights="250px">
Image:Brain sagittal section.jpg|A sagittal section of a human brain. Click this image for a high-res version in which you can read the annotations.
Image:Gray751.png|Major association fibers in the cerebrum, in a mid-sagittal lateral view.
</gallery>
</center>

There are three major types of tracts in the brain:
* '''[[w:Commissural fibers|Commissural fibers]]''' or '''transverse fibers''' connect equivalent grey matter sites in the two hemispheres of the brain.
* '''[[w:Association fiber|Association fibers]]''' connect different cortical grey matter sites to each other.
* '''[[w:Projection fibers|Projection fibers]]''' connect cortical sites to subcortical grey matter or to the spinal cord.

=== Commissural Tracts ===
; Corpus callosum (CC)
: The large tract of left-right-running fibers connecting the hemispheres. In a mid-sagittal cutting plane, it looks like a letter C turned on its side, with the tips pointing inferior; see [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p8.html]. Though the distal portions of the fibers that make up the CC are grouped into separate tracts in the interior of each hemisphere, they are collectively called the CC where they cross the mid-sagittal plane. In this sense the CC is more of a place name than a tract name; it indicates only the portions of those fibers that are near the mid-sagittal plane. Moving around the CC from the back (posterior), it is subdivided into parts named:
:; Splenium
:: The posterior, slightly bulbous part of the CC.
:; Body
:: The more-or-less flat part of the CC between the splenium and the genu.
:; Genu
:: The anterior part of the CC, where it bends back on itself. "Genu" means "knee".
:; Rostrum
:: The part of the CC inferior and posterior to the genu.
; Forceps major / forceps posterior
: The posterior projection of the CC (from the splenium) into the occipital lobe (the back of the brain). In an axial section, it looks like a letter C at the posterior portion of the brain with the tips pointing posterior. See [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p7.html].
; Forceps minor / forceps anterior
: The anterior projection of the CC (from the genu) into the cerebrum (the front of the brain). In an axial section, it looks like a letter C at the anterior portion of the brain with the tips pointing anterior. In other words, it looks sort of like a pair of mandibles over the eyes. See [http://anatomy.uams.edu/anatomyhtml/atlas_html/n1a5p7.html].
; Tapetum
: A medial projection of the CC (from the body) into the temporal lobe. In a well-reconstructed 3D tractogram, it forms a small horizontal fanning sheet of fibers emanating from the CC.

=== Association Tracts ===
; [[/Cingulum bundle|Cingulum / cingulum bundle]]
: White matter fibers located just superior to the corpus callosum, but running anterior-posterior. In a para-sagittal section, they look like a letter C turned on its side, with the tips pointing inferior, stacked right on top of the CC. In a coronal section, they look like two small circles just superior to the CC on either side of the interhemispheric fissure.
; Fornix
: C-shaped pathways that surrounds the subcortical gray matter in each hemisphere. It connects the hippocampus to the hypothalamus. Difficult to track due its curvature and partial voluming with gray matter.
; Inferior longitudinal fasciculus (ILF)
: A pathway that runs from the occipital to temporal cortices in each hemisphere. The majority of the fibers are in the temporal lobe.
; Superior longitudinal fasciculus (SLF)
: A collection of pathways that run between the frontal lobe and the temporal, parietal, and occipital lobes in each hemisphere. There are several subdivisions typically made based on their posterior connections.
:; SLF I
:: The portion of the SLF that intersects the corpus callosum and connects superior frontal cortex to parietal and occipital cortex. Typically not reconstructed with the single tensor model.
:; SLF II
:: The portion of the SLF that connects lateral frontal white matter (such as DLPFC) to the parietal and occipital cortices. Sometimes reconstructed with single tensors.
:; SLF III
:: The portion superior to the arcuate that connects lateral-inferior frontal cortex to parietal cortex. These fibers are very similar to the arcuate but do not curve.
:; Arcuate fasciculus (AF)
:: The portion of the SLF that curves to connect frontal cortex to the temporal lobe.
; Uncinate fasciculus
: A pathway that connects inferior frontal cortex to the temporal pole in each hemisphere. This curves around the insula cortex. Sometimes difficult to track due to high curvature.

=== Projection Tracts ===
; Corona radiata
: A fan-shaped sheet of WM that radiates superior (upward) from the brain stem to the cortex in each hemisphere. The fibers of the corona radiata run superior-inferior, and the fanning is anterior-posterior. The sheet is flat and thin in the left-right dimension; its orientation is approximated by a sagittal cutting plane.
; [[/Corticospinal tract|Corticospinal tract]] (CST)
: A major descending pathway that projects from the cerebral cortex to the spinal cord. It is the key pathway for voluntary movement (contrast it with the other major longitudinal but ascending pathway: the dorsal-column medial lemniscal system). Also, this is a good point to remember that tracts are generally named in source-to-target fashion. For example, corticospinal tract originates from the cortex and projects to the spinal cord, similarly corticobulbar tract goes from the cortex to the bulbar (well, brain stem), etc.
; Internal capsule
: White matter structure that runs between the cortex and medulla, containing major longitudinal (both ascending and descending) pathway systems, including the corticospinal tract, dorsal column medial lemniscus (DCML) system (only medial lemniscus part), corticobulbar tract, etc.

== Grey Matter Structures ==
; Thalamus
: Major relay nuclei (grey matter structures) in the diencephalon (division of the brain primarily containing thalamus and hypothalamus in mature brain). Most sensory information is carried to the thalamus first (i.e., via ascending tracts) and then relayed to the cerebral cortex. Similarly, neural signals controlling movements, learning, memory and emotions bound to sub-cortical structures are relayed by the thalamus to their final destinations.
; [[w:Hippocampus|Hippocampus]]
: Paired horn-shaped structures beneath the medial surface of the temporal lobes. Each half of the hippocampus is an elaboration of the edge of the cerebral cortex, where it folds up and inward from the inferior surface of the temporal lobe and curls around on itself. The hippocampus is associated with spatial memory.

== External Links ==
* [http://www.brainnav.com BrainNavigator] --- an interactive 3D atlas application with labeled brain structures and histology thumbnails for rat and mouse brains. Does not include WM structures.
* [http://braininfo.rprc.washington.edu BrainInfo] --- an interactive visual and textual guide to thousands of named anatomical structures of the macaque brain. Includes WM ''regions'' (e.g. "inferior temporal white matter") but not fascicles ("superior longitudinal fasciculus").
* [http://brainmaps.org BrainMaps.org] --- a database of histology of brains from various species, with an interactive online viewer
* [http://www.asnr2.org/neurographics/7/1/26/White%20Matter%20Tract%20Anatomy/DTI%20tutorial%201.html WM Anatomy Tutorial with DTI pictures]
* [http://www.biology-online.org/dictionary Biology-Online dictionary] --- search for text descriptions of terms
* [http://anatomy.uams.edu/anatomyhtml/neuro_atlas.html U. Arkansas neuroanatomy atlas images]
* [http://radiopaedia.org/encyclopaedia/anatomy/central-nervous-system Radiopaedia] --- a wiki encyclopedia for radiology; search for articles
* [http://www.bartleby.com/107/index.html#chap10 Gray's Anatomy] --- an illustrated anatomy textbook from 1918
* [https://www.mristudio.org MRI Studio] is a program that supposedly includes [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2478641 Mori, et al.'s 2008 multi-subject DTI-based WM atlas]

[[Category:Diffusion MRI]]

User:Jadrian Miles

2013-09-26T15:16:26Z

Jadrian Miles: /* Nifty code snippets */ rsync as a better scp

I started my PhD in CS at Brown in Fall 2006. I work on data processing, measurement, and model reconstruction from [[diffusion MRI]] of the brain.

You can find me elsewhere online:
* [http://cs.brown.edu/~jadrian CS department page]
* [http://vis.cs.brown.edu/organization/people/jadrian.html Visweb profile]
* [http://www.google.com/search?q=jadrian+miles Other places]

There are a number of directories related to me on the CS filesystem, all of which are linked from file:///map/gfx0/users/jadrian

==== Personal Documents ====
* '''Planning Documents'''
** [[/OKRs]] ([[/OKRs/Fall 2012|2012F]]) ([[/OKRs/Summer 2012|2012Sum]]) ([[/OKRs/Spring 2012|2012S]]) ([[/OKRs/Fall 2011|2011F]])
** [[:Image:Jadrian Miles PhD Proposal rev3 2010-09-10.pdf|Thesis proposal (v3, 2010-09-10)]] ([[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|v2, 2009-10-15]]) ([[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|v1, 2009-06-22]])
** [[/Paper list]]
** [[/End-of-PhD cleanup taks]]
* '''Project Notes'''
** [[/Chi-squared clustering]]
** [[/Triangle toy problem]]
** [[/vis2011 tractography statistics paper]]
** [[/Thesis manifesto: probabilistic worldview]]
* '''Archive'''
** [[/PhD Plan]]
** [[/Thesis proposal feedback]]
** [[/Research Projects]]
** [[/Diffusion simulation]]
** [[/Streamline clustering]]
** [[/Cluster slicing notes]]

==== Draft pages / notes ====
* [[/Theory Conference Deadlines]]
* [[/Plan your PhD]]
* [[/Diffusion MRI techniques]]
* [[/BB's dollarg]]
* [[/Eclipse]]
* [[/sandbox]]

==== Nifty code snippets ====
* Generate a random filename from the command line: <pre>set tmpfile=/tmp/`head -q -c 8 /proc/sys/kernel/random/uuid`</pre>
* Convert stdin to lowercase on stdout: <pre>tr '[A-Z]' '[a-z]'</pre>
* Rename files into consecutive zero-padded integers in <tt>bash</tt>: <pre>let i=0; for f in *.JPG; do mv $f `printf "%04d" $i`.jpg; let i++; done</pre>
* Test for host availability in <tt>tcsh</tt> (for loop demo; see [http://www.cyberciti.biz/faq/bash-for-loop/ here] for bash example):
<pre style="margin-left:1.5em">
foreach h ( `cat hostlist` )
ssh $h uname -n
end
</pre>
* Update a directory with stuff that exists in a CVS repository but not in the directory:
*;<pre>cvs update -d</pre>
* Concatenate PDFs (more at [http://web.archive.org/web/20090223000710/http://ansuz.sooke.bc.ca/software/pdf-append.php? the original source]; even more [http://nixtricks.wordpress.com/2009/09/01/cli-combine-or-remove-pages-from-a-pdf-document-using-ghostscript/ elsewhere], as well as [http://www.linuxjournal.com/content/tech-tip-extract-pages-pdf how to extract ranges of pages])
*;<pre>gs -q -sPAPERSIZE=letter -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=out.pdf in1.pdf in2.pdf in3.pdf ...</pre>
* Recache TeX search paths: <pre>sudo mktexlsr</pre>
* Perceptually uniform random coloring in Matlab
<pre style="margin-left:1.5em">
C = makecform('lab2srgb');
plot3(X,Y,Z,'Color', applycform([50+rand*50, -100+rand*200, -100+rand*200], C));
</pre>
* Recursively download a website using wget (see [http://www.editcorp.com/Personal/Lars_Appel/wget/wget_2.html#SEC11 the man page] for more) <pre>wget -r -np -nH http://www.site.com/subdir</pre>
* Recursively download a remote directory via SSH, preserving modification times (note the trailing slash on the remote directory!): <pre>rsync -ra -e ssh <server>:<dir>/ <local_path></pre>

==== Bookmarks ====
* [http://when2meet.com when2meet.com] --- lightweight meeting scheduling thingie

==== Tutorials ====
* [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance.htm Covariance] and [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance_matrix.htm covariance matrix]
* [http://www.tommangan.us/Tensors.pdf Tensors], by Thomas Mangan.
* [http://www.cs.ucr.edu/~vbz/resources/quatut.pdf Quaternions], by Ken Shoemake.
* [http://diglib.stanford.edu:8091/~klein/lagrange-multipliers.pdf Lagrange Multipliers], by Dan Klein.

==== Miscellaneous notes ====
* High b sensitizes to short length scale (Assaf & Cohen 1998, 2000).
* The cingulum bundle looks like a long, skinny tube (that wraps around the top and back of the CC) in a gross segmentation, and fibers run along the long axis of this tube for most of this length. Their projections into the GM, though, are actually along the side of the tube, on mid-sagittal gyri. This is a really weird shape when it comes to inferring fiber paths from the bundle shape, so it should be a smoke test for any proposed system.
* Sculpture might be a good choice for the second outside minor course. 3D reasoning, malleable shapes...

Subscribe to Test Results

2013-09-24T13:41:46Z

Jadrian Miles: Updated for clarity and a more extensive listing of files to inspect.

To add (or remove) your email to nightly test-results emails:
* Check out and/or update <code>$G/common/build/site</code> and <code>$G/common/build/valid</code> from CVS.
** In the <code>site</code> directory, look at the files <code>test.platform.cfg</code>, <code>test.platform_critical.cfg</code>, and <code>test.platform_slow.cfg</code>.
** In the <code>valid</code> directory, look at the <code>test.platform_*.cfg</code> files, particularly <code>test.platform_vrl.cfg</code>.
*** Note: I (jadrian) am not really sure whether the scripts in "valid" run, and if so, what they're for. Worth somebody investigating.
* Read the instructions in the comment at the top of each file.
* Add your name to the list of emails anywhere you would like to be notified.
* Save the files you edit, and then commit them.

=== Deprecated notes for the old version of $G ===
Tests are run daily and mail is sent when an individual tests fail.
A summary of each test run is sent as well.

* '''Subscribe to failure notifications for an individual test'''

: Checkout and carefully edit: src/gfxtest/gfxtest.cfg
: Each line specifies a test to be run and contains:

<testname> <testowners>,... <testarchs>,... <testcommand>;...

<testname> a directory in $G/src/
<testowners> subscribers for individual tests
<testarchs> linux | WIN32 | OSX | sol | sgi
<testcommand> Commands to run a test separated by a semicolon.
usually: $G/bin/gfxtest-project <projectname>

: Blank lines are permitted. There is no provision for comment lines.

* '''Subscribe to receive test summaries'''

: Checkout and carefully edit: src/gfxtest/gfxtest-nightly
: Modify the first command in the script to add the recipient's mail address.

EMAILS="you@cs.brown.edu,me@cs.brown.edu"

[[Category:$G HOWTO]][[Category:Software Development]]

User:Jadrian Miles

2013-09-20T03:51:38Z

Jadrian Miles: /* Nifty code snippets */

I started my PhD in CS at Brown in Fall 2006. I work on data processing, measurement, and model reconstruction from [[diffusion MRI]] of the brain.

You can find me elsewhere online:
* [http://cs.brown.edu/~jadrian CS department page]
* [http://vis.cs.brown.edu/organization/people/jadrian.html Visweb profile]
* [http://www.google.com/search?q=jadrian+miles Other places]

There are a number of directories related to me on the CS filesystem, all of which are linked from file:///map/gfx0/users/jadrian

==== Personal Documents ====
* '''Planning Documents'''
** [[/OKRs]] ([[/OKRs/Fall 2012|2012F]]) ([[/OKRs/Summer 2012|2012Sum]]) ([[/OKRs/Spring 2012|2012S]]) ([[/OKRs/Fall 2011|2011F]])
** [[:Image:Jadrian Miles PhD Proposal rev3 2010-09-10.pdf|Thesis proposal (v3, 2010-09-10)]] ([[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|v2, 2009-10-15]]) ([[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|v1, 2009-06-22]])
** [[/Paper list]]
** [[/End-of-PhD cleanup taks]]
* '''Project Notes'''
** [[/Chi-squared clustering]]
** [[/Triangle toy problem]]
** [[/vis2011 tractography statistics paper]]
** [[/Thesis manifesto: probabilistic worldview]]
* '''Archive'''
** [[/PhD Plan]]
** [[/Thesis proposal feedback]]
** [[/Research Projects]]
** [[/Diffusion simulation]]
** [[/Streamline clustering]]
** [[/Cluster slicing notes]]

==== Draft pages / notes ====
* [[/Theory Conference Deadlines]]
* [[/Plan your PhD]]
* [[/Diffusion MRI techniques]]
* [[/BB's dollarg]]
* [[/Eclipse]]
* [[/sandbox]]

==== Nifty code snippets ====
* Generate a random filename from the command line: <pre>set tmpfile=/tmp/`head -q -c 8 /proc/sys/kernel/random/uuid`</pre>
* Convert stdin to lowercase on stdout: <pre>tr '[A-Z]' '[a-z]'</pre>
* Rename files into consecutive zero-padded integers in <tt>bash</tt>: <pre>let i=0; for f in *.JPG; do mv $f `printf "%04d" $i`.jpg; let i++; done</pre>
* Test for host availability in <tt>tcsh</tt> (for loop demo; see [http://www.cyberciti.biz/faq/bash-for-loop/ here] for bash example):
<pre style="margin-left:1.5em">
foreach h ( `cat hostlist` )
ssh $h uname -n
end
</pre>
* Update a directory with stuff that exists in a CVS repository but not in the directory:
*;<pre>cvs update -d</pre>
* Concatenate PDFs (more at [http://web.archive.org/web/20090223000710/http://ansuz.sooke.bc.ca/software/pdf-append.php? the original source]; even more [http://nixtricks.wordpress.com/2009/09/01/cli-combine-or-remove-pages-from-a-pdf-document-using-ghostscript/ elsewhere], as well as [http://www.linuxjournal.com/content/tech-tip-extract-pages-pdf how to extract ranges of pages])
*;<pre>gs -q -sPAPERSIZE=letter -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=out.pdf in1.pdf in2.pdf in3.pdf ...</pre>
* Recache TeX search paths:
*;<pre>sudo mktexlsr</pre>
* Perceptually uniform random coloring in Matlab
<pre style="margin-left:1.5em">
C = makecform('lab2srgb');
plot3(X,Y,Z,'Color', applycform([50+rand*50, -100+rand*200, -100+rand*200], C));
</pre>
* Recursively download a website using wget (see [http://www.editcorp.com/Personal/Lars_Appel/wget/wget_2.html#SEC11 the man page] for more) <pre>wget -r -np -nH http://www.site.com/subdir</pre>

==== Bookmarks ====
* [http://when2meet.com when2meet.com] --- lightweight meeting scheduling thingie

==== Tutorials ====
* [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance.htm Covariance] and [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance_matrix.htm covariance matrix]
* [http://www.tommangan.us/Tensors.pdf Tensors], by Thomas Mangan.
* [http://www.cs.ucr.edu/~vbz/resources/quatut.pdf Quaternions], by Ken Shoemake.
* [http://diglib.stanford.edu:8091/~klein/lagrange-multipliers.pdf Lagrange Multipliers], by Dan Klein.

==== Miscellaneous notes ====
* High b sensitizes to short length scale (Assaf & Cohen 1998, 2000).
* The cingulum bundle looks like a long, skinny tube (that wraps around the top and back of the CC) in a gross segmentation, and fibers run along the long axis of this tube for most of this length. Their projections into the GM, though, are actually along the side of the tube, on mid-sagittal gyri. This is a really weird shape when it comes to inferring fiber paths from the bundle shape, so it should be a smoke test for any proposed system.
* Sculpture might be a good choice for the second outside minor course. 3D reasoning, malleable shapes...

User:Jadrian Miles

2013-05-11T20:56:36Z

Jadrian Miles: Undo revision 6307 by Jadrian Miles (talk)

I started my PhD in CS at Brown in Fall 2006. I work on data processing, measurement, and model reconstruction from [[diffusion MRI]] of the brain.

You can find me elsewhere online:
* [http://cs.brown.edu/~jadrian CS department page]
* [http://vis.cs.brown.edu/organization/people/jadrian.html Visweb profile]
* [http://www.google.com/search?q=jadrian+miles Other places]

There are a number of directories related to me on the CS filesystem, all of which are linked from file:///map/gfx0/users/jadrian

==== Personal Documents ====
* '''Planning Documents'''
** [[/OKRs]] ([[/OKRs/Fall 2012|2012F]]) ([[/OKRs/Summer 2012|2012Sum]]) ([[/OKRs/Spring 2012|2012S]]) ([[/OKRs/Fall 2011|2011F]])
** [[:Image:Jadrian Miles PhD Proposal rev3 2010-09-10.pdf|Thesis proposal (v3, 2010-09-10)]] ([[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|v2, 2009-10-15]]) ([[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|v1, 2009-06-22]])
** [[/Paper list]]
** [[/End-of-PhD cleanup taks]]
* '''Project Notes'''
** [[/Chi-squared clustering]]
** [[/Triangle toy problem]]
** [[/vis2011 tractography statistics paper]]
** [[/Thesis manifesto: probabilistic worldview]]
* '''Archive'''
** [[/PhD Plan]]
** [[/Thesis proposal feedback]]
** [[/Research Projects]]
** [[/Diffusion simulation]]
** [[/Streamline clustering]]
** [[/Cluster slicing notes]]

==== Draft pages / notes ====
* [[/Theory Conference Deadlines]]
* [[/Plan your PhD]]
* [[/Diffusion MRI techniques]]
* [[/BB's dollarg]]
* [[/Eclipse]]
* [[/sandbox]]

==== Nifty code snippets ====
* Generate a random filename from the command line: <pre>set tmpfile=/tmp/`head -q -c 8 /proc/sys/kernel/random/uuid`</pre>
* Convert stdin to lowercase on stdout: <pre>tr '[A-Z]' '[a-z]'</pre>
* Rename files into consecutive zero-padded integers in <tt>bash</tt>: <pre>let i=0; for f in *.JPG; do mv $f `printf "%04d" $i`.jpg; let i++; done</pre>
* Test for host availability in <tt>tcsh</tt> (for loop demo; see [http://www.cyberciti.biz/faq/bash-for-loop/ here] for bash example):
<pre style="margin-left:1.5em">
foreach h ( `cat hostlist` )
ssh $h uname -n
end
</pre>
* Update a directory with stuff that exists in a CVS repository but not in the directory:
*;<pre>cvs update -d</pre>
* Concatenate PDFs (more at [http://web.archive.org/web/20090223000710/http://ansuz.sooke.bc.ca/software/pdf-append.php? the original source]; even more [http://nixtricks.wordpress.com/2009/09/01/cli-combine-or-remove-pages-from-a-pdf-document-using-ghostscript/ elsewhere])
*;<pre>gs -q -sPAPERSIZE=letter -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=out.pdf in1.pdf in2.pdf in3.pdf ...</pre>
* Recache TeX search paths:
*;<pre>sudo mktexlsr</pre>
* Perceptually uniform random coloring in Matlab
<pre style="margin-left:1.5em">
C = makecform('lab2srgb');
plot3(X,Y,Z,'Color', applycform([50+rand*50, -100+rand*200, -100+rand*200], C));
</pre>
* Recursively download a website using wget (see [http://www.editcorp.com/Personal/Lars_Appel/wget/wget_2.html#SEC11 the man page] for more) <pre>wget -r -np -nH http://www.site.com/subdir</pre>

==== Bookmarks ====
* [http://when2meet.com when2meet.com] --- lightweight meeting scheduling thingie

==== Tutorials ====
* [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance.htm Covariance] and [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance_matrix.htm covariance matrix]
* [http://www.tommangan.us/Tensors.pdf Tensors], by Thomas Mangan.
* [http://www.cs.ucr.edu/~vbz/resources/quatut.pdf Quaternions], by Ken Shoemake.
* [http://diglib.stanford.edu:8091/~klein/lagrange-multipliers.pdf Lagrange Multipliers], by Dan Klein.

==== Miscellaneous notes ====
* High b sensitizes to short length scale (Assaf & Cohen 1998, 2000).
* The cingulum bundle looks like a long, skinny tube (that wraps around the top and back of the CC) in a gross segmentation, and fibers run along the long axis of this tube for most of this length. Their projections into the GM, though, are actually along the side of the tube, on mid-sagittal gyri. This is a really weird shape when it comes to inferring fiber paths from the bundle shape, so it should be a smoke test for any proposed system.
* Sculpture might be a good choice for the second outside minor course. 3D reasoning, malleable shapes...

User:Jadrian Miles

2013-05-11T20:53:32Z

Jadrian Miles: /* Personal Documents */

I started my PhD in CS at Brown in Fall 2006. I work on data processing, measurement, and model reconstruction from [[diffusion MRI]] of the brain.

You can find me elsewhere online:
* [http://cs.brown.edu/~jadrian CS department page]
* [http://vis.cs.brown.edu/organization/people/jadrian.html Visweb profile]
* [http://www.google.com/search?q=jadrian+miles Other places]

There are a number of directories related to me on the CS filesystem, all of which are linked from file:///map/gfx0/users/jadrian

==== Personal Documents ====
* '''Planning Documents'''
** [[/OKRs]] ([[/OKRs/Fall 2012|2012F]]) ([[/OKRs/Summer 2012|2012Sum]]) ([[/OKRs/Spring 2012|2012S]]) ([[/OKRs/Fall 2011|2011F]])
** [[:Image:Jadrian Miles PhD Proposal rev3 2010-09-10.pdf|Thesis proposal (v3, 2010-09-10)]] ([[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|v2, 2009-10-15]]) ([[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|v1, 2009-06-22]])
** [[/Paper list]]
** [[/End-of-PhD cleanup taks]]
* '''Project Notes'''
** [[/Voxelizer and blockhead]]
** [[/Chi-squared clustering]]
** [[/Triangle toy problem]]
** [[/vis2011 tractography statistics paper]]
** [[/Thesis manifesto: probabilistic worldview]]
* '''Archive'''
** [[/PhD Plan]]
** [[/Thesis proposal feedback]]
** [[/Research Projects]]
** [[/Diffusion simulation]]
** [[/Streamline clustering]]
** [[/Cluster slicing notes]]

==== Draft pages / notes ====
* [[/Theory Conference Deadlines]]
* [[/Plan your PhD]]
* [[/Diffusion MRI techniques]]
* [[/BB's dollarg]]
* [[/Eclipse]]
* [[/sandbox]]

==== Nifty code snippets ====
* Generate a random filename from the command line: <pre>set tmpfile=/tmp/`head -q -c 8 /proc/sys/kernel/random/uuid`</pre>
* Convert stdin to lowercase on stdout: <pre>tr '[A-Z]' '[a-z]'</pre>
* Rename files into consecutive zero-padded integers in <tt>bash</tt>: <pre>let i=0; for f in *.JPG; do mv $f `printf "%04d" $i`.jpg; let i++; done</pre>
* Test for host availability in <tt>tcsh</tt> (for loop demo; see [http://www.cyberciti.biz/faq/bash-for-loop/ here] for bash example):
<pre style="margin-left:1.5em">
foreach h ( `cat hostlist` )
ssh $h uname -n
end
</pre>
* Update a directory with stuff that exists in a CVS repository but not in the directory:
*;<pre>cvs update -d</pre>
* Concatenate PDFs (more at [http://web.archive.org/web/20090223000710/http://ansuz.sooke.bc.ca/software/pdf-append.php? the original source]; even more [http://nixtricks.wordpress.com/2009/09/01/cli-combine-or-remove-pages-from-a-pdf-document-using-ghostscript/ elsewhere])
*;<pre>gs -q -sPAPERSIZE=letter -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=out.pdf in1.pdf in2.pdf in3.pdf ...</pre>
* Recache TeX search paths:
*;<pre>sudo mktexlsr</pre>
* Perceptually uniform random coloring in Matlab
<pre style="margin-left:1.5em">
C = makecform('lab2srgb');
plot3(X,Y,Z,'Color', applycform([50+rand*50, -100+rand*200, -100+rand*200], C));
</pre>
* Recursively download a website using wget (see [http://www.editcorp.com/Personal/Lars_Appel/wget/wget_2.html#SEC11 the man page] for more) <pre>wget -r -np -nH http://www.site.com/subdir</pre>

==== Bookmarks ====
* [http://when2meet.com when2meet.com] --- lightweight meeting scheduling thingie

==== Tutorials ====
* [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance.htm Covariance] and [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance_matrix.htm covariance matrix]
* [http://www.tommangan.us/Tensors.pdf Tensors], by Thomas Mangan.
* [http://www.cs.ucr.edu/~vbz/resources/quatut.pdf Quaternions], by Ken Shoemake.
* [http://diglib.stanford.edu:8091/~klein/lagrange-multipliers.pdf Lagrange Multipliers], by Dan Klein.

==== Miscellaneous notes ====
* High b sensitizes to short length scale (Assaf & Cohen 1998, 2000).
* The cingulum bundle looks like a long, skinny tube (that wraps around the top and back of the CC) in a gross segmentation, and fibers run along the long axis of this tube for most of this length. Their projections into the GM, though, are actually along the side of the tube, on mid-sagittal gyri. This is a really weird shape when it comes to inferring fiber paths from the bundle shape, so it should be a smoke test for any proposed system.
* Sculpture might be a good choice for the second outside minor course. 3D reasoning, malleable shapes...

User:Jadrian Miles/Paper list

2013-03-15T23:46:50Z

Jadrian Miles: Added a couple more ideas inspired by the toy problem initialization and goodness-of-fit stuff

==== Curve noise statistics ====
An upgraded version of my ISMRM abstract.
* Present original findings (expanded to range over FA + MD)
** Potentially also investigate multiple algorithms: nonlinear DT fitting, multi-DT, Q-ball, other tractography algorithms, etc.
* Explain results with first-order model
* Validate the model (repeat experiment 2) on more "realistic" data with ground truth. Some options:
** Brain-based computational phantom (constructed like so: T1+HARDI scan, 2-tensor fit, tractography, filter curves for T1 termination criteria, lowpass curves, synthesize DWIs from curves)
** Popular phantom (tractography cup?)
** HARDI atlas
** Generate synthetic HARDI scans from 2-tensor fit of averaged LARDI scans for tons of healthy normals
* Prescribe a simple pipeline for deriving the noise equation for any combination of algorithms
* Maybe also consider writing up the application to PICo: probability of connection to a cortical ROI is the integral of the uncertainty PDF over that subcortical surface. But the benefit from this technique (gain in precision) may be minimal, as symmetric PDFs on either side of an ROI boundary would tend to contribute the same on either side; results might be about the same without the PDF spreading, just because you've got a lot of curves.

==== Diffusion model parsimony ====
Compare multiple diffusion models (single-tensor, multi-tensor, higher-order tensor, higher-order ODF [e.g. QBI], multi-compartment biological [e.g. CHARMED]) in terms of their "parsimony" on real data. Quantify parsimony with chi-squared goodness-of-fit on top of the probability integral transform for Rician noise. This will hopefully demonstrate that most models under- or over-fit, and that the multi-compartment models are juuuuuust right. Come to think of it, a Goldilocks reference would make for a snappy title. See dhl/cad/jadrian email from 2011-12-15 "a quickie Dagstuhl thought experiment".

Could potentially extend this to a "constructive" algorithm: something that picks the degrees of freedom for an RBF or other higher-order diffusion model.

==== Improved Hough-Peak--Finding by Topological Persistence ====
Put the toy-problem initialization technique on a solid theoretical basis. Rather than blurring the histogram, use topological persistence to disregard "sub-peaks".

==== Feature Identification in Multispectral Images Using the Hough Transform ====
Think about a "support" function for prospective line segments, with Gaussian falloff on the image plane. Finding an application area for this one might be hard.

==== Toy Problem / Probability Integral Transform ====
Write up the toy problem as an example use of the PIT in model testing for DWIs. Or maybe piggyback on Leemans/Sijbers MRM'05 synthetic DWIs from tractography, using PIT to get p-values for synthetic images. This may not be worth its own paper; maybe better to hold off on PIT stuff until it can be put in context of my own "real-problem" work.

==== Curve clustering based on chi-squared reconstruction error from a boundary model ====
I've already written up an outline of this paper. Clustering proceeds by building a boundary model of clusters/bundles, and the objective function is chi-squared goodness-of-fit derived from the tractography PDFs.

==== Automatic Shape-Sensitive Curve Clustering (§4.1.2) ====
Distance measure definition, distributed clustering algorithm, spectral clustering refinement, comparison to other techniques. Base on q-ball and DTI tractography from DTK; use Mori's atlas for ground truth? Moberts et al.'s ground truth clusterings? [moberts/van_wijk/vilanova might have a ground truth. Song Zhang had a clustering ground truth paper. Cagatay played with this at some point. bang not huge, how big is the buck? but I could be convinced -- not sure this is a vis paper? but it could be. Application of curve similarity to other areas (bat flight trajectories) would be convincing at Vis too.]

==== An Orientation-Aware Boundary Surface Representation of Space Curve Clusters ====
* '''Contributions:'''
*# "Natural" representation of clusters of curves, useful for higher-level operations. [I think that "natural" is not descriptive enough. I would try to refine that. Is the orientation a tangency constraint? There's something about it that seems important, but "orientation aware" doesn't quite seem like what it is... . I would give an example or two of the kind of higher-level operations you mean.
*# Superior results versus naive algorithms (and previously published work to solve the same problem? "Competitors" to consider include Gordon's crease surfaces, flow critical surfaces, etc. [dhl mentions Ken Joy's work...] [define "superior". Faster? more accurate? If you mean more "natural" then this may be the same thing as above]).
* '''Proofs:'''
*# Prose argument that contrasts cross-section-based boundary surfaces to other representations of curve clusters. A bunch of curves is a mess and does not lend itself to operations on the cluster volume (smoothing, joining, etc.). Median curves have no width. Rasterization creates surface artifacts and loses orientation information. Alpha shapes lose orientation information. [nice!]
*# Alpha shapes is the main "competitor". Expected results show topological defects resulting from a global choice of alpha. Run both algorithms on phantom and real data and discuss features. [I suspect that there are some other shrink-wrap approaches that might be competitors, unless alpha-shapes are always superior]

==== A Sparse, Volumetric Representation of Space Curve Clusters (§4.1.4) ====
The benefit of the initial form of the macrostructure model is its ability to reconstruct its input curves. The evaluation on this should be relatively easy, as there is no comparison to other techniques. A manual clustering is acceptable but automatic clustering that implies some bound on reconstruction error would probably be better. Good for Vis, SIGGRAPH, EG, EV, I3D, ISMRM. [but why does anyone care? This could be a way of establishing the minimal information required to represent brain datasets... but again, does anyone care about that? Must find related work. dhl suggests that this may be "importance filtering" for curves, but what's the benefit?]

==== Automatic Tractography Repair / "Healing a Broken Tractogram" ====
ISMRM poster / Neuroimage paper / TVCG paper? Demonstrate the utility of the cluster boundary surface algorithm for repairing broken curves (§4.1.5).
* '''Title, Authors''': ''"Healing a Broken DTI Tractogram with Curve Cluster Boundary Surfaces"''. Jadrian Miles and David H. Laidlaw.
* '''Contributions'''
*# A slicing-based (or alpha-shape contraction--based) algorithm for generating a cluster boundary surface with orientation, spreading, and medial axis metadata.
*# An algorithm for "sampling" novel un-broken curves from the cluster boundary surface model ("sparsifying")
*# An algorithm for extrapolating the curve cluster along its axis ("lengthening")
*# An algorithm for joining axially-aligned curve clusters based on extrapolation and refinement against underlying DWIs ("bridging")
*# Maybe others: "fattening", "smoothing"
* '''Proofs of Contributions'''
*# Demonstration (with figures) of the boundary surface algorithm on synthetic and real-world tractography data.
*# Compare the proposed algorithm (which uses only the boundary surface, not tractography curves) against one that uses barycentric coordinates of the tractography curves that form a triangle about the seed point to propagate an interpolated curve. This comparison should result in an error measure.
*# Demonstration (with figures) of the boundary extrapolation algorithm. I'm currently unaware of any competitors for this.
*# Compare against local extrapolation models: tensor deflection, linear extrapolation, cubic spline extrapolation, smoothed Bezier extrapolation. Also compare QBI tractography on HARDI data against our algorithm on angular-subsampled DTI data.
* '''Figures'''
*# Fig
*# Fig
*# Fig
* '''Related work'''
* '''Abstract'''
* '''Conclusions'''
* '''Methods'''

==== Automatic Tractography-Based DW-MRI Segmentation ====
Using DTI/QBI, automatic clustering, and simple macrostructure adjustment (dilation, splitting, merging, bridging gaps, §4.1.5), segment the WM and compare to some ground truth. Mori's atlas?

[The above two could each be ISMRM posters or talks, and should be quickly followed up by an MRM paper.]

==== A ??? (§4.2.1) ====
Generating synthetic images from the macrostructure model. Who would care about this? Possible improvement over Leemans, et al. due to gap-filling? [use data matching to support that the model is good, and wave hands about the usefulness of the higher-level model -- has a bigger bang feel than the clustering one]

[check out Ken Joy's multi-material volume representation stuff (last author) -- tvcg, I believe or maybe TOG]

User:Jadrian Miles/OKRs

2013-01-21T03:19:22Z

Jadrian Miles: Hooray! Big slicemaps work now.

Today's Date: '''{{CURRENTMONTH}}/{{CURRENTDAY2}}'''

* Meta-objective: Be ready to graduate and move on in May.
** Objective: Teach CS 931 well without it taking over my other responsibilities.
*** Key Result: Prep & teaching time are monitored throughout the semester and limited to 10 hours per week.
** Objective: Demonstrate novelty & significance of the "blockhead" method in the dissertation.
*** Key Result: Drafts for graphics- and medical-focused voxelization papers to dhl by '''01/14'''.
*** Key Result: Software generates large, multi-component slicemaps by '''01/18'''.
**** {{yellow|Completed 01/20.}}
*** Key Result: Software generates voxel maps by '''01/22'''.
*** Key Result: Software generates antialiased voxel maps by '''01/31'''.
*** Key Result: Software generates synthetic MRIs by '''02/05'''.
*** Key Result: Software generates chi-squared images by '''02/08'''.
*** Key Result: Software identifies plausible optimization moves for a two-component test dataset by '''02/13'''.
*** Key Result: Software improves objective function for two-component test dataset by '''02/15'''.
*** Key Result: Software improves objective function for fiber cup phantom by '''03/05'''.
*** Key Result: Software converges for fiber cup phantom by '''03/15'''.
*** Key result: Software improves objective function for real data by '''03/18'''.
*** Key Result: Graphics-focused paper on voxelization submitted by '''02/01'''.
*** Key Result: Medical-focused paper on voxelization submitted by '''02/22'''.
** Objective: Write and defend a dissertation that covers and synthesizes the work I've done.
*** Key Result: Dissertation chapters outlined by '''01/17'''.
**** {{green|Completed 01/16.}}
*** Key Result: Defense dates proposed to committee by '''01/17'''.
**** {{green|Completed 01/16.}}
*** Key Result: Draft dissertation to committee by '''03/20'''.
*** Key Result: [http://cs.brown.edu/degrees/doctoral/proposal/ Defense scheduled with Lauren] by '''03/20'''.
*** Key Result: Dissertation defended by '''04/30'''.
** Objective: Graduate.
*** Key Result: Dissertation [http://www.brown.edu/academics/gradschool/academics/rules-regulations/dissertation-guidelines submitted to the grad school] by '''04/30'''.
*** Key Result: Application to Graduate (and [http://brown.edu/about/commencement/graduate-school-commencement other forms]) submitted through Banner by '''04/30'''.
** Objective: Get a job.
*** Key Result: All academic job applications complete by '''01/15'''.
**** {{green|Applications complete 01/13.}}
*** Key Result: Job interviews attended as invited.
*** Key Result: Non-academic job applications in process by '''01/22'''.
** Objective: Transition smoothly out of Brown.
*** Key Result: Software and documentation archived by '''05/17'''.

Writing Make Files

2013-01-17T23:18:08Z

Jadrian Miles: Small explanation about how to use make once you've written a Makefile

The VRL has a custom system of support code for writing cross-platform, multi-compiler-version Makefiles. This helps tame the otherwise brutal strength of the [http://www.gnu.org/software/make/manual/make.html GNU Make], in which it's really easy to write unmaintainable code and shoot oneself in the foot. A Makefile that uses the G Build system will build a single directory containing one library and/or one or more programs. Projects can consist of a directory tree with a Make File in each directory.

Once you've written a Makefile in your directory, you call the command <code>make</code> to build your program. The <tt>make</tt> program runs other commands (like invoking the compiler or linker) in order, according to the instructions implicit in the Makefile.

Below is a fairly exhaustive listing of all the Make variables that you can put in your custom Makefile in order to control your build. But first you should check out the sample Makefiles for a simple '''[[Example Makefile for a program|program]]''' and '''[[Example Makefile for a library|library]]'''.

Just working from the examples, it's straightforward to get started building your program ''so long as it is located in a standard sandbox directory''. See the [[Software Development|software development documentation]] for more details. However, if you are new to Make, you may find it useful to familiarize yourself with it. Make is a fairly user hostile language. The semantics are difficult to learn and error messages tend to be uninformative. However, Make is a language that is hard to avoid so most programmers become familiar with it. The G Build system uses Gnu make as it has consistent behavior over many platforms. So when please take the time to [http://www.gnu.org/software/make/manual/make.html read the official documentation] or [http://www.google.com/search?q=gnu+make+tutorial find a good tutorial].

=== '''Make File Contents''' ===

* '''Make Variable Settings'''

[[G_COMPILER]] = <Compiler Version> Designate a compiler and version.
[[PROJECT]] = <Project Name> Required project name.
[[PROJECT_HOME]] = <Root Directory> Subdirectories reference the project root.

[[LIBRARY]] = <Library Name> Use when the directory contains a library.
[[CXXSRC]] = <C++ Source>.cpp ... List C++ source files for a library.
[[CSRC]] = <C Source>.c ... List C source files for a library.
[[INCLUDE_H]] = <C/C++ Header> ... List public library headers to install.

[[PROGRAM]] = <Program Name> ... List each program in the directory.
[[CXX]]<Program> = <C++ Source>.cpp ... List C++ source files for a program.
[[C]]<Program> = <C Source>.c ... List C source files for a program.

[[G_USE]] = <Package Name> ... Predefined settings for packages.
[[LDLIB_VER]] = <Library Name> ... Link a program with a library.
[[LDLIB_PROJECT]] = <Project Name> ... Add a project library to the search path.

* '''Variable Settings For Experts'''
[[BIN_SCRIPT]] += <Script Files> ... Install files in the bin directory.
[[SHARE_FILE]] += <Shared Files> ... Install files in the share directory.

[[LDLIB]] += <Linker Setting> ... Pass libraries directly to the linker.
[[CXXFLAGS]] += <C++ Compiler Flag> ... Pass flags directly to the C++ compiler.
[[CFLAGS]] += <C Compiler Flag> ... Pass flags directly to the C compiler.
[[CXXINC]] += <Include Directory> ... Pass includes directly to the C++ compiler.
[[CINC]] += <Include Directory> ... Pass includes directly to the C compiler.

Always add this include statement to bring in the G Build make files.

<pre>
include $(G)/common/build/make/directory.make
</pre>

Optionally add this include statement to build using all available compilers. Note that when including this make file additional targets are declared for:<br>
:::install all allclean

<pre>
include $(G)/common/build/make/build.multiple.make
</pre>

* '''Directory Access variables'''

These variables can be used to access directories to avoid using hard coded paths. Do not set these variables.

[[G_IMPORT]] Location where third party software is installed.
[[G_INSTALL]] Location where files are installed with "make install".

=== '''Projects With Multiple Directories''' ===

Projects can contain a directory tree that can be organized any way the developers chooses. Make files using the Build system each build a single directory in the tree. By convention the default Make target ("make" with no operand) will build the current directory for a single compiler. By convention an "all" target will build the current directory and all of it's subdirectories.

Usually Makefiles in a directory above several subdirectories will use Gnu Make commands to build the subdirectories. In this case you won't need to include the '''directory.make''' file. Here are some typical Gnu Make commands you might want to use:

<pre>
# Require that the all targets always be used.
#
default:
@echo "Use: make all"

clean:
@echo "Use: make allclean"

test:
@echo "Use: make alltest"
</pre>

<pre>
# Create a target to clean all the subdirectories.
#
allclean:
$(MAKE) -C utility allclean
$(MAKE) -C library allclean
$(MAKE) -C program allclean
</pre>

<pre>
# Create a target to build one subdirectory.
#
.PHONY: utility
utility:
$(MAKE) -C utility all
</pre>

Only a small subset of Unix Utilities is included in the G Build system. Limiting the use of Unix commands in rules makes it easier to get a project developed on Unix to work on native Windows. Complex commands can invoke scripts. Python is recommended as you can use it to easily write platform independent scripts with good error reporting.

Writing Make Files

2013-01-17T23:16:23Z

Jadrian Miles:

The VRL has a custom system of support code for writing cross-platform, multi-compiler-version Makefiles. This helps tame the otherwise brutal strength of the [http://www.gnu.org/software/make/manual/make.html GNU Make], in which it's really easy to write unmaintainable code and shoot oneself in the foot. A Makefile that uses the G Build system will build a single directory containing one library and/or one or more programs. Projects can consist of a directory tree with a Make File in each directory.

Once you've written a Makefile in your directory, you call the command <tt>make</tt> to build the program according to the instructions implicit in the Makefile.

Below is a fairly exhaustive listing of all the Make variables that you can put in your custom Makefile in order to control your build. But first you should check out the sample Makefiles for a simple '''[[Example Makefile for a program|program]]''' and '''[[Example Makefile for a library|library]]'''.

Just working from the examples, it's straightforward to get started building your program ''so long as it is located in a standard sandbox directory''. See the [[Software Development|software development documentation]] for more details. However, if you are new to Make, you may find it useful to familiarize yourself with it. Make is a fairly user hostile language. The semantics are difficult to learn and error messages tend to be uninformative. However, Make is a language that is hard to avoid so most programmers become familiar with it. The G Build system uses Gnu make as it has consistent behavior over many platforms. So when please take the time to [http://www.gnu.org/software/make/manual/make.html read the official documentation] or [http://www.google.com/search?q=gnu+make+tutorial find a good tutorial].

=== '''Make File Contents''' ===

* '''Make Variable Settings'''

[[G_COMPILER]] = <Compiler Version> Designate a compiler and version.
[[PROJECT]] = <Project Name> Required project name.
[[PROJECT_HOME]] = <Root Directory> Subdirectories reference the project root.

[[LIBRARY]] = <Library Name> Use when the directory contains a library.
[[CXXSRC]] = <C++ Source>.cpp ... List C++ source files for a library.
[[CSRC]] = <C Source>.c ... List C source files for a library.
[[INCLUDE_H]] = <C/C++ Header> ... List public library headers to install.

[[PROGRAM]] = <Program Name> ... List each program in the directory.
[[CXX]]<Program> = <C++ Source>.cpp ... List C++ source files for a program.
[[C]]<Program> = <C Source>.c ... List C source files for a program.

[[G_USE]] = <Package Name> ... Predefined settings for packages.
[[LDLIB_VER]] = <Library Name> ... Link a program with a library.
[[LDLIB_PROJECT]] = <Project Name> ... Add a project library to the search path.

* '''Variable Settings For Experts'''
[[BIN_SCRIPT]] += <Script Files> ... Install files in the bin directory.
[[SHARE_FILE]] += <Shared Files> ... Install files in the share directory.

[[LDLIB]] += <Linker Setting> ... Pass libraries directly to the linker.
[[CXXFLAGS]] += <C++ Compiler Flag> ... Pass flags directly to the C++ compiler.
[[CFLAGS]] += <C Compiler Flag> ... Pass flags directly to the C compiler.
[[CXXINC]] += <Include Directory> ... Pass includes directly to the C++ compiler.
[[CINC]] += <Include Directory> ... Pass includes directly to the C compiler.

Always add this include statement to bring in the G Build make files.

<pre>
include $(G)/common/build/make/directory.make
</pre>

Optionally add this include statement to build using all available compilers. Note that when including this make file additional targets are declared for:<br>
:::install all allclean

<pre>
include $(G)/common/build/make/build.multiple.make
</pre>

* '''Directory Access variables'''

These variables can be used to access directories to avoid using hard coded paths. Do not set these variables.

[[G_IMPORT]] Location where third party software is installed.
[[G_INSTALL]] Location where files are installed with "make install".

=== '''Projects With Multiple Directories''' ===

Projects can contain a directory tree that can be organized any way the developers chooses. Make files using the Build system each build a single directory in the tree. By convention the default Make target ("make" with no operand) will build the current directory for a single compiler. By convention an "all" target will build the current directory and all of it's subdirectories.

Usually Makefiles in a directory above several subdirectories will use Gnu Make commands to build the subdirectories. In this case you won't need to include the '''directory.make''' file. Here are some typical Gnu Make commands you might want to use:

<pre>
# Require that the all targets always be used.
#
default:
@echo "Use: make all"

clean:
@echo "Use: make allclean"

test:
@echo "Use: make alltest"
</pre>

<pre>
# Create a target to clean all the subdirectories.
#
allclean:
$(MAKE) -C utility allclean
$(MAKE) -C library allclean
$(MAKE) -C program allclean
</pre>

<pre>
# Create a target to build one subdirectory.
#
.PHONY: utility
utility:
$(MAKE) -C utility all
</pre>

Only a small subset of Unix Utilities is included in the G Build system. Limiting the use of Unix commands in rules makes it easier to get a project developed on Unix to work on native Windows. Complex commands can invoke scripts. Python is recommended as you can use it to easily write platform independent scripts with good error reporting.

Example Makefile for a program

2013-01-17T23:14:33Z

Jadrian Miles:

<pre>
# G_COMPILER settings are optional, but can be used to designate a preferred compiler.
# If they are set here you won't need to set them outside the Makefile.
#
ifeq ($(GARCH),linux)
G_COMPILER ?= gcc4
endif
ifeq ($(GARCH),WIN32)
G_COMPILER ?= cl9
endif

# The project name is used to create directory names. For consistency
# make this the same name as the top level directory for the project.
#
PROJECT = marklar

# For a project with subdirectories the PROJECT_HOME variable is the path
# of the top level directory in the project. In a simple project there
# is only the top level directory and this setting is not needed.
#
PROJECT_HOME = $(realpath ./)

# This is the name of the generated executable file.
# There can be more than one program listed per directory.
#
PROGRAM = myProgram

# For each program with C++ sources set a variable using the program name.
# By convention the source file containing the "main" entry point has the
# same name as the program.
#
CXXmyProgram = myProgram.cpp mySubroutine.cpp

# For each program with C sources set a variable using the program name.
#
CmyProgram = myUtility.c

# The libraries g3d, vrg3d, and cg have preset declarations to make them
# easy to set up.
#
G_USE = vrg3d

# If you want to link with libraries built using the G Build make files
# use the LDLIB_VER variable. This ensures you will link against the
# version that was built with the same compiler as your program.
#
LDLIB_VER = is3d mri nr

# If you want to add some targets other than the defaults
# use raw make commands. Note that if you want to make a program
# installable you need to declare and install target as shown.
#
all: directory

allclean: clean

install: installprog

# This brings in the G Build make files and is required.
#
include $(G)/common/build/make/directory.make
</pre>

Example Makefile for a library

2013-01-17T23:14:25Z

Jadrian Miles:

<pre>
# G_COMPILER settings are optional, but are handy if you want to designate a
# preferred compiler. If they are set here you won't need to set them outside
# the Makefile. Generally a library is built with all available compilers.
# This gives users the freedom to use the compiler of their choice.
#
ifeq ($(GARCH),linux)
G_COMPILER ?= gcc4
endif
ifeq ($(GARCH),WIN32)
G_COMPILER ?= cl9
endif

# The project name is used to create directory names. For consistency
# make this the same name as the top level directory for the project.
#
PROJECT = collection

# For a project with subdirectories the PROJECT_HOME variable is the path
# of the top level directory in the project. In a simple project there
# is only the top level directory and this setting is not needed.
#
PROJECT_HOME = $(realpath ./)

# This is the name of the generated library file.
# There can be more only one library per directory.
#
LIBRARY = crest

# For C++ sources in a library set the CXXSRC variable.
#
CXXSRC = crest.cpp subroutine.cpp

# For C sources in a library set the CSRC variable.
#
CSRC = utility.c

# Include files to be installed. Do not list include files
# that are private.
#
INCLUDE_H = subroutine.h utility.h

# This include brings in the G Build Make files and is required.
#
include $(G)/common/build/make/directory.make

# This include brings in Make declarations to build a library
# with all available compilers. Note that when you include
# this make file additional targets are declared for:
# install all allclean
#
include $(G)/common/build/make/build.multiple.make
</pre>

Writing Make Files

2013-01-17T23:14:11Z

Jadrian Miles: Cleaned up intro text

The VRL has a custom system of support code for writing cross-platform, multi-compiler-version Makefiles. This helps tame the otherwise brutal strength of the [http://www.gnu.org/software/make/manual/make.html GNU Make], in which it's really easy to write unmaintainable code and shoot oneself in the foot. A Makefile that uses the G Build system will build a single directory containing one library and/or one or more programs. Projects can consist of a directory tree with a Make File in each directory.

Below is a fairly exhaustive listing of all the Make variables that you can put in your custom Makefile in order to control your build. But first you should check out the sample Makefiles for a simple '''[[Example Makefile for a program|program]]''' and '''[[Example Makefile for a library|library]]'''.

Just working from the examples, it's straightforward to get started building your program ''so long as it is located in a standard sandbox directory''. See the [[Software Development|software development documentation]] for more details. However, if you are new to Make, you may find it useful to familiarize yourself with it. Make is a fairly user hostile language. The semantics are difficult to learn and error messages tend to be uninformative. However, Make is a language that is hard to avoid so most programmers become familiar with it. The G Build system uses Gnu make as it has consistent behavior over many platforms. So when please take the time to [http://www.gnu.org/software/make/manual/make.html read the official documentation] or [http://www.google.com/search?q=gnu+make+tutorial find a good tutorial].

=== '''Make File Contents''' ===

* '''Make Variable Settings'''

[[G_COMPILER]] = <Compiler Version> Designate a compiler and version.
[[PROJECT]] = <Project Name> Required project name.
[[PROJECT_HOME]] = <Root Directory> Subdirectories reference the project root.

[[LIBRARY]] = <Library Name> Use when the directory contains a library.
[[CXXSRC]] = <C++ Source>.cpp ... List C++ source files for a library.
[[CSRC]] = <C Source>.c ... List C source files for a library.
[[INCLUDE_H]] = <C/C++ Header> ... List public library headers to install.

[[PROGRAM]] = <Program Name> ... List each program in the directory.
[[CXX]]<Program> = <C++ Source>.cpp ... List C++ source files for a program.
[[C]]<Program> = <C Source>.c ... List C source files for a program.

[[G_USE]] = <Package Name> ... Predefined settings for packages.
[[LDLIB_VER]] = <Library Name> ... Link a program with a library.
[[LDLIB_PROJECT]] = <Project Name> ... Add a project library to the search path.

* '''Variable Settings For Experts'''
[[BIN_SCRIPT]] += <Script Files> ... Install files in the bin directory.
[[SHARE_FILE]] += <Shared Files> ... Install files in the share directory.

[[LDLIB]] += <Linker Setting> ... Pass libraries directly to the linker.
[[CXXFLAGS]] += <C++ Compiler Flag> ... Pass flags directly to the C++ compiler.
[[CFLAGS]] += <C Compiler Flag> ... Pass flags directly to the C compiler.
[[CXXINC]] += <Include Directory> ... Pass includes directly to the C++ compiler.
[[CINC]] += <Include Directory> ... Pass includes directly to the C compiler.

Always add this include statement to bring in the G Build make files.

<pre>
include $(G)/common/build/make/directory.make
</pre>

Optionally add this include statement to build using all available compilers. Note that when including this make file additional targets are declared for:<br>
:::install all allclean

<pre>
include $(G)/common/build/make/build.multiple.make
</pre>

* '''Directory Access variables'''

These variables can be used to access directories to avoid using hard coded paths. Do not set these variables.

[[G_IMPORT]] Location where third party software is installed.
[[G_INSTALL]] Location where files are installed with "make install".

=== '''Projects With Multiple Directories''' ===

Projects can contain a directory tree that can be organized any way the developers chooses. Make files using the Build system each build a single directory in the tree. By convention the default Make target ("make" with no operand) will build the current directory for a single compiler. By convention an "all" target will build the current directory and all of it's subdirectories.

Usually Makefiles in a directory above several subdirectories will use Gnu Make commands to build the subdirectories. In this case you won't need to include the '''directory.make''' file. Here are some typical Gnu Make commands you might want to use:

<pre>
# Require that the all targets always be used.
#
default:
@echo "Use: make all"

clean:
@echo "Use: make allclean"

test:
@echo "Use: make alltest"
</pre>

<pre>
# Create a target to clean all the subdirectories.
#
allclean:
$(MAKE) -C utility allclean
$(MAKE) -C library allclean
$(MAKE) -C program allclean
</pre>

<pre>
# Create a target to build one subdirectory.
#
.PHONY: utility
utility:
$(MAKE) -C utility all
</pre>

Only a small subset of Unix Utilities is included in the G Build system. Limiting the use of Unix commands in rules makes it easier to get a project developed on Unix to work on native Windows. Complex commands can invoke scripts. Python is recommended as you can use it to easily write platform independent scripts with good error reporting.

Program

2013-01-17T23:13:37Z

Jadrian Miles: moved Program to Example Makefile for a program: Terrible page name. wtf?

#REDIRECT [[Example Makefile for a program]]

Example Makefile for a program

2013-01-17T23:13:37Z

Jadrian Miles: moved Program to Example Makefile for a program: Terrible page name. wtf?

== Example of a Makefile for a simple program ==

<pre>
# G_COMPILER settings are optional, but can be used to designate a preferred compiler.
# If they are set here you won't need to set them outside the Makefile.
#
ifeq ($(GARCH),linux)
G_COMPILER ?= gcc4
endif
ifeq ($(GARCH),WIN32)
G_COMPILER ?= cl9
endif

# The project name is used to create directory names. For consistency
# make this the same name as the top level directory for the project.
#
PROJECT = marklar

# For a project with subdirectories the PROJECT_HOME variable is the path
# of the top level directory in the project. In a simple project there
# is only the top level directory and this setting is not needed.
#
PROJECT_HOME = $(realpath ./)

# This is the name of the generated executable file.
# There can be more than one program listed per directory.
#
PROGRAM = myProgram

# For each program with C++ sources set a variable using the program name.
# By convention the source file containing the "main" entry point has the
# same name as the program.
#
CXXmyProgram = myProgram.cpp mySubroutine.cpp

# For each program with C sources set a variable using the program name.
#
CmyProgram = myUtility.c

# The libraries g3d, vrg3d, and cg have preset declarations to make them
# easy to set up.
#
G_USE = vrg3d

# If you want to link with libraries built using the G Build make files
# use the LDLIB_VER variable. This ensures you will link against the
# version that was built with the same compiler as your program.
#
LDLIB_VER = is3d mri nr

# If you want to add some targets other than the defaults
# use raw make commands. Note that if you want to make a program
# installable you need to declare and install target as shown.
#
all: directory

allclean: clean

install: installprog

# This brings in the G Build make files and is required.
#
include $(G)/common/build/make/directory.make
</pre>

Library

2013-01-17T23:12:42Z

Jadrian Miles: moved Library to Example Makefile for a library: Poorly named.

#REDIRECT [[Example Makefile for a library]]

Example Makefile for a library

2013-01-17T23:12:42Z

Jadrian Miles: moved Library to Example Makefile for a library: Poorly named.

== Example of a Makefile for a simple library ==

<pre>
# G_COMPILER settings are optional, but are handy if you want to designate a
# preferred compiler. If they are set here you won't need to set them outside
# the Makefile. Generally a library is built with all available compilers.
# This gives users the freedom to use the compiler of their choice.
#
ifeq ($(GARCH),linux)
G_COMPILER ?= gcc4
endif
ifeq ($(GARCH),WIN32)
G_COMPILER ?= cl9
endif

# The project name is used to create directory names. For consistency
# make this the same name as the top level directory for the project.
#
PROJECT = collection

# For a project with subdirectories the PROJECT_HOME variable is the path
# of the top level directory in the project. In a simple project there
# is only the top level directory and this setting is not needed.
#
PROJECT_HOME = $(realpath ./)

# This is the name of the generated library file.
# There can be more only one library per directory.
#
LIBRARY = crest

# For C++ sources in a library set the CXXSRC variable.
#
CXXSRC = crest.cpp subroutine.cpp

# For C sources in a library set the CSRC variable.
#
CSRC = utility.c

# Include files to be installed. Do not list include files
# that are private.
#
INCLUDE_H = subroutine.h utility.h

# This include brings in the G Build Make files and is required.
#
include $(G)/common/build/make/directory.make

# This include brings in Make declarations to build a library
# with all available compilers. Note that when you include
# this make file additional targets are declared for:
# install all allclean
#
include $(G)/common/build/make/build.multiple.make
</pre>

User:Jadrian Miles/OKRs

2013-01-17T00:08:30Z

Jadrian Miles:

Today's Date: '''{{CURRENTMONTH}}/{{CURRENTDAY2}}'''

* Meta-objective: Be ready to graduate and move on in May.
** Objective: Teach CS 931 well without it taking over my other responsibilities.
*** Key Result: Prep & teaching time are monitored throughout the semester and limited to 10 hours per week.
** Objective: Demonstrate novelty & significance of the "blockhead" method in the dissertation.
*** Key Result: Drafts for graphics- and medical-focused voxelization papers to dhl by '''01/14'''.
*** Key Result: Software generates large, multi-component slicemaps by '''01/18'''.
*** Key Result: Software generates voxel maps by '''01/22'''.
*** Key Result: Software generates antialiased voxel maps by '''01/31'''.
*** Key Result: Software generates synthetic MRIs by '''02/05'''.
*** Key Result: Software generates chi-squared images by '''02/08'''.
*** Key Result: Software identifies plausible optimization moves for a two-component test dataset by '''02/13'''.
*** Key Result: Software improves objective function for two-component test dataset by '''02/15'''.
*** Key Result: Software improves objective function for fiber cup phantom by '''03/05'''.
*** Key Result: Software converges for fiber cup phantom by '''03/15'''.
*** Key result: Software improves objective function for real data by '''03/18'''.
*** Key Result: Graphics-focused paper on voxelization submitted by '''02/01'''.
*** Key Result: Medical-focused paper on voxelization submitted by '''02/22'''.
** Objective: Write and defend a dissertation that covers and synthesizes the work I've done.
*** Key Result: Dissertation chapters outlined by '''01/17'''.
**** {{green|Completed 01/16.}}
*** Key Result: Defense dates proposed to committee by '''01/17'''.
**** {{green|Completed 01/16.}}
*** Key Result: Draft dissertation to committee by '''03/20'''.
*** Key Result: [http://cs.brown.edu/degrees/doctoral/proposal/ Defense scheduled with Lauren] by '''03/20'''.
*** Key Result: Dissertation defended by '''04/30'''.
** Objective: Graduate.
*** Key Result: Dissertation [http://www.brown.edu/academics/gradschool/academics/rules-regulations/dissertation-guidelines submitted to the grad school] by '''04/30'''.
*** Key Result: Application to Graduate (and [http://brown.edu/about/commencement/graduate-school-commencement other forms]) submitted through Banner by '''04/30'''.
** Objective: Get a job.
*** Key Result: All academic job applications complete by '''01/15'''.
**** {{green|Applications complete 01/13.}}
*** Key Result: Job interviews attended as invited.
*** Key Result: Non-academic job applications in process by '''01/22'''.
** Objective: Transition smoothly out of Brown.
*** Key Result: Software and documentation archived by '''05/17'''.

User:Jadrian Miles/OKRs

2013-01-15T23:17:52Z

Jadrian Miles: Tweaked some dates and added more milestones in response to dhl meeting

Today's Date: '''{{CURRENTMONTH}}/{{CURRENTDAY2}}'''

* Meta-objective: Be ready to graduate and move on in May.
** Objective: Teach CS 931 well without it taking over my other responsibilities.
*** Key Result: Prep & teaching time are monitored throughout the semester and limited to 6 hours per week.
** Objective: Demonstrate novelty & significance of the "blockhead" method in the dissertation.
*** Key Result: Drafts for graphics- and medical-focused voxelization papers to dhl by '''01/14'''.
*** Key Result: Software generates large, multi-component slicemaps by '''01/18'''.
*** Key Result: Software generates voxel maps by '''01/22'''.
*** Key Result: Software generates antialiased voxel maps by '''01/31'''.
*** Key Result: Software generates synthetic MRIs by '''02/05'''.
*** Key Result: Software generates chi-squared images by '''02/08'''.
*** Key Result: Software identifies plausible optimization moves for a two-component test dataset by '''02/13'''.
*** Key Result: Software improves objective function for two-component test dataset by '''02/15'''.
*** Key Result: Software improves objective function for fiber cup phantom by '''03/05'''.
*** Key Result: Software converges for fiber cup phantom by '''03/15'''.
*** Key result: Software improves objective function for real data by '''03/18'''.
*** Key Result: Graphics-focused paper on voxelization submitted by '''02/01'''.
*** Key Result: Medical-focused paper on voxelization submitted by '''02/22'''.
** Objective: Write and defend a dissertation that covers and synthesizes the work I've done.
*** Key Result: Dissertation chapters outlined by '''01/17'''.
*** Key Result: Defense dates proposed to committee by '''01/17'''.
*** Key Result: Draft dissertation to committee by '''03/20'''.
*** Key Result: [http://cs.brown.edu/degrees/doctoral/proposal/ Defense scheduled with Lauren] by '''03/20'''.
*** Key Result: Dissertation defended by '''04/30'''.
** Objective: Graduate.
*** Key Result: Dissertation [http://www.brown.edu/academics/gradschool/academics/rules-regulations/dissertation-guidelines submitted to the grad school] by '''04/30'''.
*** Key Result: Application to Graduate (and [http://brown.edu/about/commencement/graduate-school-commencement other forms]) submitted through Banner by '''04/30'''.
** Objective: Get a job.
*** Key Result: All academic job applications complete by '''01/15'''.
**** {{green|Applications complete 01/13.}}
*** Key Result: Job interviews attended as invited.
*** Key Result: Non-academic job applications in process by '''01/22'''.
** Objective: Transition smoothly out of Brown.
*** Key Result: Software and documentation archived by '''05/17'''.

User:Jadrian Miles/OKRs

2013-01-15T15:54:25Z

Jadrian Miles:

Today's Date: '''{{CURRENTMONTH}}/{{CURRENTDAY2}}'''

* Meta-objective: Be ready to graduate and move on in May.
** Objective: Teach CS 931 well without it taking over my other responsibilities.
*** Key Result: Prep & teaching time are monitored throughout the semester and limited to 6 hours per week.
** Objective: Demonstrate novelty & significance of the "blockhead" method in the dissertation.
*** Key Result: Drafts for graphics- and medical-focused voxelization papers to dhl by '''01/14'''.
*** Key Result: Software generates large, multi-component slicemaps by '''01/18'''.
*** Key Result: Software generates voxel maps by '''01/22'''.
*** Key Result: Software generates antialiased voxel maps by '''01/31'''.
*** Key Result: Software generates synthetic MRIs by '''02/05'''.
*** Key Result: Software generates chi-squared images by '''02/08'''.
*** Key Result: Software identifies plausible optimization moves for a two-component test dataset by '''02/13'''.
*** Key Result: Software improves objective function for two-component test dataset by '''02/15'''.
*** Key Result: Graphics-focused paper on voxelization submitted by '''02/01'''.
*** Key Result: Medical-focused paper on voxelization submitted by '''02/22'''.
** Objective: Write and defend a dissertation that covers and synthesizes the work I've done.
*** Key Result: Draft dissertation to committee by '''03/09'''.
*** Key Result: Defense dates proposed to committee by '''03/09'''.
*** Key Result: Defense scheduled with Lauren by '''03/16'''.
*** Key Result: Dissertation defended by '''04/16'''.
** Objective: Graduate.
*** Key Result: Dissertation [http://www.brown.edu/academics/gradschool/academics/rules-regulations/dissertation-guidelines submitted to the grad school] by '''04/31'''.
*** Key Result: Application to Graduate (and [http://brown.edu/about/commencement/graduate-school-commencement other forms]) submitted through Banner by '''04/31'''.
** Objective: Get a job.
*** Key Result: All academic job applications complete by '''01/15'''.
**** {{green|Applications complete 01/13.}}
*** Key Result: Job interviews attended as invited.
*** Key Result: Non-academic job applications in process by '''01/22'''.
** Objective: Transition smoothly out of Brown.
*** Key Result: Software and documentation archived by '''05/17'''.

Plans and Goals

2013-01-10T21:25:44Z

Jadrian Miles: Forgot to change the current semester to Spring 2013

On this page the members of the [[VRL]] record and refine their goals for the current semester. This is a living document in which [[dhl]] will provide feedback. See the bottom of the page for links to past plans & goals documents.

== Current Schedule ==
Meetings are on Mondays. The authoritative list is in dhl's calendar.

== Current Plans and Goals (Spring '13) ==

=== [[User:Connor Gramazio|Connor]] ===
* Take courses.
** Interdisciplinary SciVis
** Distributed Databases and Systems
** Computational Biology
** Reading & Research: HCI/Viz course reading from last year
** Independent brush up on probability. Min = follow CSCI45 lectures. Max = do all p-sets and programming.
* Use classes and additional reading to come up with research proposal.
** By the end of the semester have a rough draft of my proposal finished
* Revisit the areas of interest I wrote down for David's class at the end of the semester. Reevaluate them, adding and subtracting as appropriate. My hope is that this will make me more aware of what research topics I am interested in.
** Designing interactive visualizations to support big data
** Building visualization software that solves real problems
** Making visualizations accessible to everyone
* Read through the VisWeek 2012 proceedings.



----

=== [[User:David Laidlaw|David]] ===

* keep grad students moving along
* keep Cave project moving along (Facilities groundbreaking (delivery dates)
** facilities budget solid and approved
** permit applied for
** facilites work done, including floor delivery and installation
** metal fab parts completed, delivered, assembled
** create demo group
* excellent cs237
* prep for cool, new(ish?) cs16 for Spring
* December Expeditions in Computing submission
* volume rendering interaction in WristVis
* brain metrics papers out with Ryan
* longer-term funding matched with group



----

=== [[User:Jadrian Miles|Jadrian]] ===

* [[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Initial thesis proposal, submitted 2009-06-22]]
* [[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|Proposal second revision, prepared 2009-10-15]]

{{User:Jadrian Miles/OKRs}}


----

=== [[User:Nathan Malkin|Nathan]] ===



----

=== [[User:Steven Gomez|Steve]] ===
* Give a good InfoVis talk in Seattle on Oct 16
* Help cs237 be successful as a TA

* Keep IVRG on track toward an eventual VisWeek or CG+A project
** Design and pilot user study by end of semester

* Proposal
** scheduled for mid-semester
** final document revised with feedback from committee (draft 3 by Sep 28, any changes made by presentation time)
** presented to committee

* Hands-on research
** Pilot WebGL tractography task on Turk by Nov
** Evaluation-example search tool online by Oct 13 (Visweek start); try discuss w/ others at BELIV workshop at VisWeek
** Draft of CG+A paper submitted by Dec 20



----

=== [[User:Ryan Cabeen|Ryan]] ===

* Start thesis proposal
** Choose committee
** Choose topic
** Conduct preliminary work
* Brain Imaging
** Run South Africa through pipeline
** Run St Louis 2nd timepoint through pipeline
** Manually select tracts for evaluation of automated tract pipeline
** Develop web-based circle vis
** Send out Edinburgh normal study paper
* Big Data Vis
** Make reading list
** Continue work with Jian developing visual interface to SciDB
** Design DB structure for the brain imaging projects
** Explore ideas: collaboration, caching, suggestions, level of detail, CAVE applications, user studies



----

=== [[User:Hua Guo|Hua]] ===

* Required coursework: complete two CS courses (or three)
** Topics in Distributed Databases and System (big data analysis focus!)
** Computational Photography
** Human Factors and Interface Design (just sitting-in, perhaps)
* Progress on the research comp
** Implement the interface with support for user goals
** Do the user study
** Submit to CHI as a work-in-progress



----

== Past Plans and Goals ==
* [[/Fall 2012|Fall '12]]
* [[/Summer 2012|Summer '12]]
* [[/Spring 2012|Spring '12]]
* [[/Summer-Fall 2011|Summer-Fall '11]]
* [[/Spring 2011|Spring '11]]
* [[/Summer-Fall 2010|Summer-Fall '10]]
* [[/Spring 2010|Spring '10]]
* [[/Fall 2009|Fall '09]]
* [[/Summer 2009|Summer '09]]
* [[/Spring 2009|Spring '09]]
* [[/Fall 2008|Fall '08]]
* [http://sites.google.com/a/vis.cs.brown.edu/collaboravis/Home/summer-08-group-goals Summer '08]

[[Category:VRL]]

Plans and Goals

2013-01-10T21:25:16Z

Jadrian Miles: Updated slightly to prepare for new semester

On this page the members of the [[VRL]] record and refine their goals for the current semester. This is a living document in which [[dhl]] will provide feedback. See the bottom of the page for links to past plans & goals documents.

== Current Schedule ==
Meetings are on Mondays. The authoritative list is in dhl's calendar.

== Current Plans and Goals (Fall '12) ==

=== [[User:Connor Gramazio|Connor]] ===
* Take courses.
** Interdisciplinary SciVis
** Distributed Databases and Systems
** Computational Biology
** Reading & Research: HCI/Viz course reading from last year
** Independent brush up on probability. Min = follow CSCI45 lectures. Max = do all p-sets and programming.
* Use classes and additional reading to come up with research proposal.
** By the end of the semester have a rough draft of my proposal finished
* Revisit the areas of interest I wrote down for David's class at the end of the semester. Reevaluate them, adding and subtracting as appropriate. My hope is that this will make me more aware of what research topics I am interested in.
** Designing interactive visualizations to support big data
** Building visualization software that solves real problems
** Making visualizations accessible to everyone
* Read through the VisWeek 2012 proceedings.



----

=== [[User:David Laidlaw|David]] ===

* keep grad students moving along
* keep Cave project moving along (Facilities groundbreaking (delivery dates)
** facilities budget solid and approved
** permit applied for
** facilites work done, including floor delivery and installation
** metal fab parts completed, delivered, assembled
** create demo group
* excellent cs237
* prep for cool, new(ish?) cs16 for Spring
* December Expeditions in Computing submission
* volume rendering interaction in WristVis
* brain metrics papers out with Ryan
* longer-term funding matched with group



----

=== [[User:Jadrian Miles|Jadrian]] ===

* [[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Initial thesis proposal, submitted 2009-06-22]]
* [[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|Proposal second revision, prepared 2009-10-15]]

{{User:Jadrian Miles/OKRs}}


----

=== [[User:Nathan Malkin|Nathan]] ===



----

=== [[User:Steven Gomez|Steve]] ===
* Give a good InfoVis talk in Seattle on Oct 16
* Help cs237 be successful as a TA

* Keep IVRG on track toward an eventual VisWeek or CG+A project
** Design and pilot user study by end of semester

* Proposal
** scheduled for mid-semester
** final document revised with feedback from committee (draft 3 by Sep 28, any changes made by presentation time)
** presented to committee

* Hands-on research
** Pilot WebGL tractography task on Turk by Nov
** Evaluation-example search tool online by Oct 13 (Visweek start); try discuss w/ others at BELIV workshop at VisWeek
** Draft of CG+A paper submitted by Dec 20



----

=== [[User:Ryan Cabeen|Ryan]] ===

* Start thesis proposal
** Choose committee
** Choose topic
** Conduct preliminary work
* Brain Imaging
** Run South Africa through pipeline
** Run St Louis 2nd timepoint through pipeline
** Manually select tracts for evaluation of automated tract pipeline
** Develop web-based circle vis
** Send out Edinburgh normal study paper
* Big Data Vis
** Make reading list
** Continue work with Jian developing visual interface to SciDB
** Design DB structure for the brain imaging projects
** Explore ideas: collaboration, caching, suggestions, level of detail, CAVE applications, user studies



----

=== [[User:Hua Guo|Hua]] ===

* Required coursework: complete two CS courses (or three)
** Topics in Distributed Databases and System (big data analysis focus!)
** Computational Photography
** Human Factors and Interface Design (just sitting-in, perhaps)
* Progress on the research comp
** Implement the interface with support for user goals
** Do the user study
** Submit to CHI as a work-in-progress



----

== Past Plans and Goals ==
* [[/Fall 2012|Fall '12]]
* [[/Summer 2012|Summer '12]]
* [[/Spring 2012|Spring '12]]
* [[/Summer-Fall 2011|Summer-Fall '11]]
* [[/Spring 2011|Spring '11]]
* [[/Summer-Fall 2010|Summer-Fall '10]]
* [[/Spring 2010|Spring '10]]
* [[/Fall 2009|Fall '09]]
* [[/Summer 2009|Summer '09]]
* [[/Spring 2009|Spring '09]]
* [[/Fall 2008|Fall '08]]
* [http://sites.google.com/a/vis.cs.brown.edu/collaboravis/Home/summer-08-group-goals Summer '08]

[[Category:VRL]]

Plans and Goals/Fall 2012

2013-01-10T21:19:17Z

Jadrian Miles: /* Jadrian */

=== [[User:Cagatay Demiralp|Çağatay]] ===

* Finish thesis
** Model Selection
** Topology
* Send the revised article on theory of visualization to CG & A


----

=== Connor ===
<ul>
<li>Take courses.<br />
<ul>
<li>Interdisciplinary SciVis</li>
<li>Distributed Databases and Systems</li>
<li>Computational Biology</li>
<li>Reading & Research: HCI/Viz course reading from last year</li>
<li>Independent brush up on probability. Min = follow CSCI45 lectures. Max = do all p-sets and programming.</li>
</ul>
</li>
<li>Use classes and additional reading to come up with research proposal.<br />
<ul>
<li>By the end of the semester have a rough draft of my proposal finished</li>
</ul>
</li>
<li>Revisit the areas of interest I wrote down for David's class at the end of the semester. Reevaluate them, adding and subtracting as appropriate. My hope is that this will make me more aware of what research topics I am interested in.<br/>
<ul>
<li>Designing interactive visualizations to support big data</li>
<li>Building visualization software that solves real problems</li>
<li>Making visualizations accessible to everyone</li>
</ul></li>
<li>Read through the VisWeek 2012 proceedings.</li>
</ul>


----

=== David ===

* keep grad students moving along
* keep Cave project moving along (Facilities groundbreaking (delivery dates)
** facilities budget solid and approved
** permit applied for
** facilites work done, including floor delivery and installation
** metal fab parts completed, delivered, assembled
** create demo group
* excellent cs237
* prep for cool, new(ish?) cs16 for Spring
* December Expeditions in Computing submission
* volume rendering interaction in WristVis
* brain metrics papers out with Ryan
* longer-term funding matched with group



----

=== [[User:Jadrian Miles|Jadrian]] ===

* [[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Initial thesis proposal, submitted 2009-06-22]]
* [[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|Proposal second revision, prepared 2009-10-15]]

{{User:Jadrian Miles/OKRs/Fall 2012}}


----

=== Nathan ===



----

=== [[User:Steven Gomez|Steve]] ===
* Give a good InfoVis talk in Seattle on Oct 16
* Help cs237 be successful as a TA

* Keep IVRG on track toward an eventual VisWeek or CG+A project
** Design and pilot user study by end of semester

* Proposal
** scheduled for mid-semester
** final document revised with feedback from committee (draft 3 by Sep 28, any changes made by presentation time)
** presented to committee

* Hands-on research
** Pilot WebGL tractography task on Turk by Nov
** Evaluation-example search tool online by Oct 13 (Visweek start); try discuss w/ others at BELIV workshop at VisWeek
** Draft of CG+A paper submitted by Dec 20



----

=== Ryan ===

* Start thesis proposal
** Choose committee
** Choose topic
** Conduct preliminary work
* Brain Imaging
** Run South Africa through pipeline
** Run St Louis 2nd timepoint through pipeline
** Manually select tracts for evaluation of automated tract pipeline
** Develop web-based circle vis
** Send out Edinburgh normal study paper
* Big Data Vis
** Make reading list
** Continue work with Jian developing visual interface to SciDB
** Design DB structure for the brain imaging projects
** Explore ideas: collaboration, caching, suggestions, level of detail, CAVE applications, user studies



----

=== [[User:Hua Guo|Hua]] ===

* Required coursework: complete two CS courses (or three)
** Topics in Distributed Databases and System (big data analysis focus!)
** Computational Photography
** Human Factors and Interface Design (just sitting-in, perhaps)
* Progress on the research comp
** Implement the interface with support for user goals
** Do the user study
** Submit to CHI as a work-in-progress

Plans and Goals/Fall 2012

2013-01-10T21:18:55Z

Jadrian Miles: Created page with "=== Çağatay === * Finish thesis ** Model Selection ** Topology * Send the revised article on theory of visualization to CG & A <!-- please do..."

=== [[User:Cagatay Demiralp|Çağatay]] ===

* Finish thesis
** Model Selection
** Topology
* Send the revised article on theory of visualization to CG & A


----

=== Connor ===
<ul>
<li>Take courses.<br />
<ul>
<li>Interdisciplinary SciVis</li>
<li>Distributed Databases and Systems</li>
<li>Computational Biology</li>
<li>Reading & Research: HCI/Viz course reading from last year</li>
<li>Independent brush up on probability. Min = follow CSCI45 lectures. Max = do all p-sets and programming.</li>
</ul>
</li>
<li>Use classes and additional reading to come up with research proposal.<br />
<ul>
<li>By the end of the semester have a rough draft of my proposal finished</li>
</ul>
</li>
<li>Revisit the areas of interest I wrote down for David's class at the end of the semester. Reevaluate them, adding and subtracting as appropriate. My hope is that this will make me more aware of what research topics I am interested in.<br/>
<ul>
<li>Designing interactive visualizations to support big data</li>
<li>Building visualization software that solves real problems</li>
<li>Making visualizations accessible to everyone</li>
</ul></li>
<li>Read through the VisWeek 2012 proceedings.</li>
</ul>


----

=== David ===

* keep grad students moving along
* keep Cave project moving along (Facilities groundbreaking (delivery dates)
** facilities budget solid and approved
** permit applied for
** facilites work done, including floor delivery and installation
** metal fab parts completed, delivered, assembled
** create demo group
* excellent cs237
* prep for cool, new(ish?) cs16 for Spring
* December Expeditions in Computing submission
* volume rendering interaction in WristVis
* brain metrics papers out with Ryan
* longer-term funding matched with group



----

=== [[User:Jadrian Miles|Jadrian]] ===

* [[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Initial thesis proposal, submitted 2009-06-22]]
* [[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|Proposal second revision, prepared 2009-10-15]]

{{User:Jadrian Miles/OKRs}}


----

=== Nathan ===



----

=== [[User:Steven Gomez|Steve]] ===
* Give a good InfoVis talk in Seattle on Oct 16
* Help cs237 be successful as a TA

* Keep IVRG on track toward an eventual VisWeek or CG+A project
** Design and pilot user study by end of semester

* Proposal
** scheduled for mid-semester
** final document revised with feedback from committee (draft 3 by Sep 28, any changes made by presentation time)
** presented to committee

* Hands-on research
** Pilot WebGL tractography task on Turk by Nov
** Evaluation-example search tool online by Oct 13 (Visweek start); try discuss w/ others at BELIV workshop at VisWeek
** Draft of CG+A paper submitted by Dec 20



----

=== Ryan ===

* Start thesis proposal
** Choose committee
** Choose topic
** Conduct preliminary work
* Brain Imaging
** Run South Africa through pipeline
** Run St Louis 2nd timepoint through pipeline
** Manually select tracts for evaluation of automated tract pipeline
** Develop web-based circle vis
** Send out Edinburgh normal study paper
* Big Data Vis
** Make reading list
** Continue work with Jian developing visual interface to SciDB
** Design DB structure for the brain imaging projects
** Explore ideas: collaboration, caching, suggestions, level of detail, CAVE applications, user studies



----

=== [[User:Hua Guo|Hua]] ===

* Required coursework: complete two CS courses (or three)
** Topics in Distributed Databases and System (big data analysis focus!)
** Computational Photography
** Human Factors and Interface Design (just sitting-in, perhaps)
* Progress on the research comp
** Implement the interface with support for user goals
** Do the user study
** Submit to CHI as a work-in-progress

Plans and Goals

2013-01-10T21:18:05Z

Jadrian Miles: /* Past Plans and Goals */ made a new archive page

On this page the members of the [[VRL]] record and refine their goals for the current semester. This is a living document in which [[dhl]] will provide feedback. See the bottom of the page for links to past plans & goals documents.

== Current Schedule ==
Meetings are on Tuesdays. The authoritative list is in dhl's calendar. (updated here 9/24/10)

== Current Plans and Goals (Fall '12) ==

=== [[User:Cagatay Demiralp|Çağatay]] ===

* Finish thesis
** Model Selection
** Topology
* Send the revised article on theory of visualization to CG & A


----

=== Connor ===
<ul>
<li>Take courses.<br />
<ul>
<li>Interdisciplinary SciVis</li>
<li>Distributed Databases and Systems</li>
<li>Computational Biology</li>
<li>Reading & Research: HCI/Viz course reading from last year</li>
<li>Independent brush up on probability. Min = follow CSCI45 lectures. Max = do all p-sets and programming.</li>
</ul>
</li>
<li>Use classes and additional reading to come up with research proposal.<br />
<ul>
<li>By the end of the semester have a rough draft of my proposal finished</li>
</ul>
</li>
<li>Revisit the areas of interest I wrote down for David's class at the end of the semester. Reevaluate them, adding and subtracting as appropriate. My hope is that this will make me more aware of what research topics I am interested in.<br/>
<ul>
<li>Designing interactive visualizations to support big data</li>
<li>Building visualization software that solves real problems</li>
<li>Making visualizations accessible to everyone</li>
</ul></li>
<li>Read through the VisWeek 2012 proceedings.</li>
</ul>


----

=== David ===

* keep grad students moving along
* keep Cave project moving along (Facilities groundbreaking (delivery dates)
** facilities budget solid and approved
** permit applied for
** facilites work done, including floor delivery and installation
** metal fab parts completed, delivered, assembled
** create demo group
* excellent cs237
* prep for cool, new(ish?) cs16 for Spring
* December Expeditions in Computing submission
* volume rendering interaction in WristVis
* brain metrics papers out with Ryan
* longer-term funding matched with group



----

=== [[User:Jadrian Miles|Jadrian]] ===

* [[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Initial thesis proposal, submitted 2009-06-22]]
* [[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|Proposal second revision, prepared 2009-10-15]]

{{User:Jadrian Miles/OKRs}}


----

=== Nathan ===



----

=== [[User:Steven Gomez|Steve]] ===
* Give a good InfoVis talk in Seattle on Oct 16
* Help cs237 be successful as a TA

* Keep IVRG on track toward an eventual VisWeek or CG+A project
** Design and pilot user study by end of semester

* Proposal
** scheduled for mid-semester
** final document revised with feedback from committee (draft 3 by Sep 28, any changes made by presentation time)
** presented to committee

* Hands-on research
** Pilot WebGL tractography task on Turk by Nov
** Evaluation-example search tool online by Oct 13 (Visweek start); try discuss w/ others at BELIV workshop at VisWeek
** Draft of CG+A paper submitted by Dec 20



----

=== Ryan ===

* Start thesis proposal
** Choose committee
** Choose topic
** Conduct preliminary work
* Brain Imaging
** Run South Africa through pipeline
** Run St Louis 2nd timepoint through pipeline
** Manually select tracts for evaluation of automated tract pipeline
** Develop web-based circle vis
** Send out Edinburgh normal study paper
* Big Data Vis
** Make reading list
** Continue work with Jian developing visual interface to SciDB
** Design DB structure for the brain imaging projects
** Explore ideas: collaboration, caching, suggestions, level of detail, CAVE applications, user studies



----

=== [[User:Hua Guo|Hua]] ===

* Required coursework: complete two CS courses (or three)
** Topics in Distributed Databases and System (big data analysis focus!)
** Computational Photography
** Human Factors and Interface Design (just sitting-in, perhaps)
* Progress on the research comp
** Implement the interface with support for user goals
** Do the user study
** Submit to CHI as a work-in-progress



----

== Past Plans and Goals ==
* [[/Fall 2012|Fall '12]]
* [[/Summer 2012|Summer '12]]
* [[/Spring 2012|Spring '12]]
* [[/Summer-Fall 2011|Summer-Fall '11]]
* [[/Spring 2011|Spring '11]]
* [[/Summer-Fall 2010|Summer-Fall '10]]
* [[/Spring 2010|Spring '10]]
* [[/Fall 2009|Fall '09]]
* [[/Summer 2009|Summer '09]]
* [[/Spring 2009|Spring '09]]
* [[/Fall 2008|Fall '08]]
* [http://sites.google.com/a/vis.cs.brown.edu/collaboravis/Home/summer-08-group-goals Summer '08]

[[Category:VRL]]

User:Jadrian Miles/OKRs

2013-01-10T21:17:30Z

Jadrian Miles: New OKRs for Spring 2013

Today's Date: '''{{CURRENTMONTH}}/{{CURRENTDAY2}}'''

* Meta-objective: Be ready to graduate and move on in May.
** Objective: Teach CS 931 well without it taking over my other responsibilities.
*** Key Result: Prep & teaching time are monitored throughout the semester and limited to 6 hours per week.
** Objective: Demonstrate novelty & significance of the "blockhead" method in the dissertation.
*** Key Result: Drafts for graphics- and medical-focused voxelization papers to dhl by '''01/14'''.
*** Key Result: Software generates large, multi-component slicemaps by '''01/18'''.
*** Key Result: Software generates voxel maps by '''01/22'''.
*** Key Result: Software generates antialiased voxel maps by '''01/31'''.
*** Key Result: Software generates synthetic MRIs by '''02/05'''.
*** Key Result: Software generates chi-squared images by '''02/08'''.
*** Key Result: Software identifies plausible optimization moves for a two-component test dataset by '''02/13'''.
*** Key Result: Software improves objective function for two-component test dataset by '''02/15'''.
*** Key Result: Graphics-focused paper on voxelization submitted by '''02/01'''.
*** Key Result: Medical-focused paper on voxelization submitted by '''02/22'''.
** Objective: Write and defend a dissertation that covers and synthesizes the work I've done.
*** Key Result: Draft dissertation to committee by '''03/09'''.
*** Key Result: Defense dates proposed to committee by '''03/09'''.
*** Key Result: Defense scheduled with Lauren by '''03/16'''.
*** Key Result: Dissertation defended by '''04/16'''.
** Objective: Graduate.
*** Key Result: Dissertation [http://www.brown.edu/academics/gradschool/academics/rules-regulations/dissertation-guidelines submitted to the grad school] by '''04/31'''.
*** Key Result: Application to Graduate (and [http://brown.edu/about/commencement/graduate-school-commencement other forms]) submitted through Banner by '''04/31'''.
** Objective: Get a job.
*** Key Result: All academic job applications complete by '''01/15'''.
*** Key Result: Job interviews attended as invited.
*** Key Result: Non-academic job applications in process by '''01/22'''.
** Objective: Transition smoothly out of Brown.
*** Key Result: Software and documentation archived by '''05/17'''.

User:Jadrian Miles/OKRs/Fall 2012

2013-01-10T16:54:18Z

Jadrian Miles: Created page with "* Meta-objective: Be ready to defend by March. ** Objective: Write a dissertation that covers and synthesizes the work I've done. ** Objective: Salvage something dissertation-..."

* Meta-objective: Be ready to defend by March.
** Objective: Write a dissertation that covers and synthesizes the work I've done.
** Objective: Salvage something dissertation-worthy from the tract-noise experiments.
** Objective: Demonstrate novelty & significance of the "blockhead" method in the dissertation.

User:Jadrian Miles

2013-01-10T16:53:56Z

Jadrian Miles: /* Personal Documents */

I started my PhD in CS at Brown in Fall 2006. I work on data processing, measurement, and model reconstruction from [[diffusion MRI]] of the brain.

You can find me elsewhere online:
* [http://cs.brown.edu/~jadrian CS department page]
* [http://vis.cs.brown.edu/organization/people/jadrian.html Visweb profile]
* [http://www.google.com/search?q=jadrian+miles Other places]

There are a number of directories related to me on the CS filesystem, all of which are linked from file:///map/gfx0/users/jadrian

==== Personal Documents ====
* '''Planning Documents'''
** [[/OKRs]] ([[/OKRs/Fall 2012|2012F]]) ([[/OKRs/Summer 2012|2012Sum]]) ([[/OKRs/Spring 2012|2012S]]) ([[/OKRs/Fall 2011|2011F]])
** [[:Image:Jadrian Miles PhD Proposal rev3 2010-09-10.pdf|Thesis proposal (v3, 2010-09-10)]] ([[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|v2, 2009-10-15]]) ([[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|v1, 2009-06-22]])
** [[/Paper list]]
** [[/End-of-PhD cleanup taks]]
* '''Project Notes'''
** [[/Chi-squared clustering]]
** [[/Triangle toy problem]]
** [[/vis2011 tractography statistics paper]]
** [[/Thesis manifesto: probabilistic worldview]]
* '''Archive'''
** [[/PhD Plan]]
** [[/Thesis proposal feedback]]
** [[/Research Projects]]
** [[/Diffusion simulation]]
** [[/Streamline clustering]]
** [[/Cluster slicing notes]]

==== Draft pages / notes ====
* [[/Theory Conference Deadlines]]
* [[/Plan your PhD]]
* [[/Diffusion MRI techniques]]
* [[/BB's dollarg]]
* [[/Eclipse]]
* [[/sandbox]]

==== Nifty code snippets ====
* Generate a random filename from the command line: <pre>set tmpfile=/tmp/`head -q -c 8 /proc/sys/kernel/random/uuid`</pre>
* Convert stdin to lowercase on stdout: <pre>tr '[A-Z]' '[a-z]'</pre>
* Rename files into consecutive zero-padded integers in <tt>bash</tt>: <pre>let i=0; for f in *.JPG; do mv $f `printf "%04d" $i`.jpg; let i++; done</pre>
* Test for host availability in <tt>tcsh</tt> (for loop demo; see [http://www.cyberciti.biz/faq/bash-for-loop/ here] for bash example):
<pre style="margin-left:1.5em">
foreach h ( `cat hostlist` )
ssh $h uname -n
end
</pre>
* Update a directory with stuff that exists in a CVS repository but not in the directory:
*;<pre>cvs update -d</pre>
* Concatenate PDFs (more at [http://web.archive.org/web/20090223000710/http://ansuz.sooke.bc.ca/software/pdf-append.php? the original source]; even more [http://nixtricks.wordpress.com/2009/09/01/cli-combine-or-remove-pages-from-a-pdf-document-using-ghostscript/ elsewhere])
*;<pre>gs -q -sPAPERSIZE=letter -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=out.pdf in1.pdf in2.pdf in3.pdf ...</pre>
* Recache TeX search paths:
*;<pre>sudo mktexlsr</pre>
* Perceptually uniform random coloring in Matlab
<pre style="margin-left:1.5em">
C = makecform('lab2srgb');
plot3(X,Y,Z,'Color', applycform([50+rand*50, -100+rand*200, -100+rand*200], C));
</pre>
* Recursively download a website using wget (see [http://www.editcorp.com/Personal/Lars_Appel/wget/wget_2.html#SEC11 the man page] for more) <pre>wget -r -np -nH http://www.site.com/subdir</pre>

==== Bookmarks ====
* [http://when2meet.com when2meet.com] --- lightweight meeting scheduling thingie

==== Tutorials ====
* [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance.htm Covariance] and [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance_matrix.htm covariance matrix]
* [http://www.tommangan.us/Tensors.pdf Tensors], by Thomas Mangan.
* [http://www.cs.ucr.edu/~vbz/resources/quatut.pdf Quaternions], by Ken Shoemake.
* [http://diglib.stanford.edu:8091/~klein/lagrange-multipliers.pdf Lagrange Multipliers], by Dan Klein.

==== Miscellaneous notes ====
* High b sensitizes to short length scale (Assaf & Cohen 1998, 2000).
* The cingulum bundle looks like a long, skinny tube (that wraps around the top and back of the CC) in a gross segmentation, and fibers run along the long axis of this tube for most of this length. Their projections into the GM, though, are actually along the side of the tube, on mid-sagittal gyri. This is a really weird shape when it comes to inferring fiber paths from the bundle shape, so it should be a smoke test for any proposed system.
* Sculpture might be a good choice for the second outside minor course. 3D reasoning, malleable shapes...

File:Shoemake - Quaternions.pdf

2012-12-20T21:41:14Z

Jadrian Miles: "Quaternions", a tutorial by Ken Shoemake.

"Quaternions", a tutorial by Ken Shoemake.

File:Mangan - Tensors.pdf

2012-12-20T20:56:39Z

Jadrian Miles: "A Gentle Introduction to Tensors", a tutorial by Thomas Mangan.

"A Gentle Introduction to Tensors", a tutorial by Thomas Mangan.

File:Klein - Lagrange Multipliers.pdf

2012-12-20T20:52:04Z

Jadrian Miles: "Lagrange Multipliers Without Permanent Scarring", a tutorial by Dan Klein.

"Lagrange Multipliers Without Permanent Scarring", a tutorial by Dan Klein.

User:Jadrian Miles

2012-12-20T20:14:48Z

Jadrian Miles: /* Tutorials */

I started my PhD in CS at Brown in Fall 2006. I work on data processing, measurement, and model reconstruction from [[diffusion MRI]] of the brain.

You can find me elsewhere online:
* [http://cs.brown.edu/~jadrian CS department page]
* [http://vis.cs.brown.edu/organization/people/jadrian.html Visweb profile]
* [http://www.google.com/search?q=jadrian+miles Other places]

There are a number of directories related to me on the CS filesystem, all of which are linked from file:///map/gfx0/users/jadrian

==== Personal Documents ====
* '''Planning Documents'''
** [[/OKRs]] ([[/OKRs/Summer 2012|2012Sum]]) ([[/OKRs/Spring 2012|2012S]]) ([[/OKRs/Fall 2011|2011F]])
** [[:Image:Jadrian Miles PhD Proposal rev3 2010-09-10.pdf|Thesis proposal (v3, 2010-09-10)]] ([[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|v2, 2009-10-15]]) ([[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|v1, 2009-06-22]])
** [[/Paper list]]
** [[/End-of-PhD cleanup taks]]
* '''Project Notes'''
** [[/Chi-squared clustering]]
** [[/Triangle toy problem]]
** [[/vis2011 tractography statistics paper]]
** [[/Thesis manifesto: probabilistic worldview]]
* '''Archive'''
** [[/PhD Plan]]
** [[/Thesis proposal feedback]]
** [[/Research Projects]]
** [[/Diffusion simulation]]
** [[/Streamline clustering]]
** [[/Cluster slicing notes]]

==== Draft pages / notes ====
* [[/Theory Conference Deadlines]]
* [[/Plan your PhD]]
* [[/Diffusion MRI techniques]]
* [[/BB's dollarg]]
* [[/Eclipse]]
* [[/sandbox]]

==== Nifty code snippets ====
* Generate a random filename from the command line: <pre>set tmpfile=/tmp/`head -q -c 8 /proc/sys/kernel/random/uuid`</pre>
* Convert stdin to lowercase on stdout: <pre>tr '[A-Z]' '[a-z]'</pre>
* Rename files into consecutive zero-padded integers in <tt>bash</tt>: <pre>let i=0; for f in *.JPG; do mv $f `printf "%04d" $i`.jpg; let i++; done</pre>
* Test for host availability in <tt>tcsh</tt> (for loop demo; see [http://www.cyberciti.biz/faq/bash-for-loop/ here] for bash example):
<pre style="margin-left:1.5em">
foreach h ( `cat hostlist` )
ssh $h uname -n
end
</pre>
* Update a directory with stuff that exists in a CVS repository but not in the directory:
*;<pre>cvs update -d</pre>
* Concatenate PDFs (more at [http://web.archive.org/web/20090223000710/http://ansuz.sooke.bc.ca/software/pdf-append.php? the original source]; even more [http://nixtricks.wordpress.com/2009/09/01/cli-combine-or-remove-pages-from-a-pdf-document-using-ghostscript/ elsewhere])
*;<pre>gs -q -sPAPERSIZE=letter -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=out.pdf in1.pdf in2.pdf in3.pdf ...</pre>
* Recache TeX search paths:
*;<pre>sudo mktexlsr</pre>
* Perceptually uniform random coloring in Matlab
<pre style="margin-left:1.5em">
C = makecform('lab2srgb');
plot3(X,Y,Z,'Color', applycform([50+rand*50, -100+rand*200, -100+rand*200], C));
</pre>
* Recursively download a website using wget (see [http://www.editcorp.com/Personal/Lars_Appel/wget/wget_2.html#SEC11 the man page] for more) <pre>wget -r -np -nH http://www.site.com/subdir</pre>

==== Bookmarks ====
* [http://when2meet.com when2meet.com] --- lightweight meeting scheduling thingie

==== Tutorials ====
* [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance.htm Covariance] and [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance_matrix.htm covariance matrix]
* [http://www.tommangan.us/Tensors.pdf Tensors], by Thomas Mangan.
* [http://www.cs.ucr.edu/~vbz/resources/quatut.pdf Quaternions], by Ken Shoemake.
* [http://diglib.stanford.edu:8091/~klein/lagrange-multipliers.pdf Lagrange Multipliers], by Dan Klein.

==== Miscellaneous notes ====
* High b sensitizes to short length scale (Assaf & Cohen 1998, 2000).
* The cingulum bundle looks like a long, skinny tube (that wraps around the top and back of the CC) in a gross segmentation, and fibers run along the long axis of this tube for most of this length. Their projections into the GM, though, are actually along the side of the tube, on mid-sagittal gyri. This is a really weird shape when it comes to inferring fiber paths from the bundle shape, so it should be a smoke test for any proposed system.
* Sculpture might be a good choice for the second outside minor course. 3D reasoning, malleable shapes...

Give a talk

2012-09-23T22:44:46Z

Jadrian Miles: /* Presentation Style and Audience Interaction */ more on pointers

This page presents advice on how to give a successful talk. You will likely give many different types of talks during your time at Brown: informal elevator talks, social discussions at parties, fast-forwards during CS orientation, [[SciVis Meetings|sciviz lunch talks]] (which have their own explicit [[SciVis Meetings#Rubric for SciVis Talks|evaluation rubric]]), poster presentations at conferences, full talks at conferences, research comps proposals and defenses, thesis proposals and defenses. Each of these requires some unique understanding, but all of them share many common points. The advice below generally concerns hour-long talks, but can be adapted to any talk.

The central piece of advice, from which all the bits below may be derived, is this: '''the audience is always right'''. A talk may be about you and your work, but its real purpose is to convey ideas to your audience and to gather feedback from them. Your audience wants you to be clear, concise, efficient, and respectful. They want to feel like they understand what you're talking about, and they don't want you to waste their time or confuse them. The audience's interpretation of the talk ''is'' the reality of the talk. If you make a point but fail to convey it to the audience, you haven't really made your point. So always think about your audience when designing and refining your talk, and try to anticipate what they care about and what they'll be thinking while attending your talk.

== Talk Structure and Content ==
=== Aim for an Audience ===
* '''Know who your audience is''' and tailor your talk to this audience. Different audiences expect different talk structures, expect emphasis on different points, make different assumptions, know different background, etc. When building or editing your talk, critically ask yourself: "does my audience ''understand'' this point?" "Does my audience ''care'' about this point?" Leave out details that your audience doesn't care about (as they might serve only to confuse, distract, or take time away in your talk). Make sure to include details that your audience does care about.
** To find out who your audience will be, ask around with people who have given a similar talk at the same venue. On rare occasions, it can happen that you actually ''can't'' make a good guess about who your audience will be; for example, when you find out at the last minute that a much larger and more general audience will be attending your talk than you were told to expect. In this case, it's essential to gauge your audience's comprehension of your talk ''as you're giving it'', and adjust on the fly. See the points below about "checkpoints" and asking questions.
** ''Pro tip'': your audience for a proposal or defense is the ''faculty''. Each audience member therefore: has deep knowledge about a particular computer science subfield not necessarily related to yours, has a general knowledge of computer science, thinks about problems from a technical/algorithmic/data-oriented perspective, and is probably pretty geeky and detail-oriented. They will ask deep, probing, and potentially picky questions. Organize your talk to minimize confusion for this audience, and avoid irrelevant details that members of the audience might latch onto.
** ''Bonus pro tip'': think very explicitly about '''your goals for the talk'''. What do you want to convey to the audience? In most high-stakes talks, it's not just some fact that you worked out through your research. Other goals might include: "I want the audience to believe that I know what I'm doing." "I want my committee to let me graduate." Write these goals down and ask yourself whether the things you do and talk about in your talk serve them.
* '''Don't give the same talk to two different audiences'''. The point of a talk is to convey an idea to an audience. Each different audience has a different way of receiving ideas. This means that if you give a talk to two different audiences, it should not be the same talk, even if (to your mind) it's on the same subject.
* '''Understand the heterogeneity of your audience'''. No matter how uniform an audience might seem to be, it still contains different sub-groups. For example, for a thesis proposal presentation, your audience is composed of computer scientists, but it includes people from disciplines as diverse as natural language processing, computation theory, computational biology, and computer vision. For a presentation at an interdisciplinary conference (Vis or ISMRM, for example), your audience includes people from computer science as well as one or more application areas, and each of these communities has sub-communities (researchers vs. clinicians vs. engineers, for example).
* '''Be careful about terminology''' that means different things to different communities. Either be very explicit about the definitions of your terms, use unambiguous plain-language terms, or just drop them entirely and figure out a different way to present your point. An example list of problematic terms includes "greedy", "Monte Carlo", "solve", "optimal", "energy", "experiment", "model", "fit". If you're certain of the composition of your audience, some jargon of this sort may be acceptable, but remember that audiences are often more heterogeneous than you might think.

=== Make Them Care ===
* '''Tell them a story / put it in context'''. Your work will be most engaging when your audience understands as quickly as possible its basic context or purpose. You can achieve this by giving a simple example problem that motivates your work, an example of how someone would use your work, or an example of what your work looks like. If you can get people to care about your work in thirty seconds, put those thirty seconds at the beginning of your talk.
* '''Emphasize contributions, not design process'''. When working on a research agenda that includes multiple contributions, you may conceive of it as a sequence of experiments that you learn things from, where each experiment develops into or informs the development of the next. It's tempting to present your research in this way, to show it as a sequence of intellectual developments, but this is a mistake. Contributions are a concise and discrete way for outsiders to think about someone else's research; they provide a consistent framework in which your audience can understand the scope and impact of your work.
** If you're really itching to talk about your design process, present each research item as a separate entity and discuss intellectual connections between them as a secondary point, later in the talk.
* '''Clearly formulate a "problem statement" for each contribution'''. The truth may be messier, but for the purposes of presenting research, it's important to summarize any given contribution in terms of the problem it aims to solve, its data inputs and outputs, and how you prove your contribution. This gives your audience the understanding necessary to truly engage with your work and to think critically about it.
* '''Show concrete examples'''. Your audience will understand what you're doing better if they have a clear picture in their minds of the format of your data and problem, inputs and outputs. Unless your audience is composed of people who have the same background as you, there will be some basic point that you have to explain before getting into the specifics of your work. If you work with medical images and you're talking to a non-medical audience, show an example image. If you work with visualizations and you're talking to a non-viz audience, show some canonical examples. When reviewing results, the same thing goes: show concrete examples at the level of detail appropriate for your audience, whether illustrations, screenshots, charts, tables, or something else.
* '''Don't overstate your case'''. Explicitly establish the assumptions built into your work and the scope of your hypotheses and conclusions. Think like a scientist or mathematician and be very conservative: unless you specify the scope of your statements, it may be assumed that they apply universally, which is almost always not the case.
* '''Don't understate your case'''. Don't state your hypotheses, conclusions, or contributions with such general language that they don't actually claim anything. Be specific about the work that you did (or will do) and point out (implicitly or explicitly) its novelty and significance.
* '''Clearly establish novelty and significance'''. If your audience doesn't know the related work that you're trying to improve on, show it to them and make it clear why your work is an improvement. A comparison table is a great way to do this; greater still is a comparison table with p-values.

=== Help Them Understand ===
* '''Number your slides'''. This way, audience members who want to ask questions about specific slides can note the slide number, to make the Q&A go more smoothly.
* '''Build in checkpoints'''. A "checkpoint" is a specific time in the talk where you want to make sure your audience is caught up. For example, if concept A may be difficult for your audience to understand but is essential for understanding concept B, put a checkpoint between the explanations of the two concepts. At this checkpoint, put an overview of concept A on the slide, and plan to ask your audience if they understand it.
* '''Clearly distinguish "figures" from "illustrations"'''. Figures and illustrations are two different types of pictures. A figure is a picture that relates in a concrete and preferably quantifiable way to the work or point that you're presenting. An illustration is a generic picture that is evocative of the concept you're discussing. Trouble arises when a picture that you intend as an illustration gets misinterpreted by your audience as a figure. For example, this could happen with a bar chart. You may mean to present it as merely an example of a result that one ''might'' get, or a way that one ''might'' care to present a certain class of data, but if your audience identifies it as a figure instead, they will immediately start digging for details that will aid in its interpretation in terms of your work. This can almost fatally derail a talk. Try hard to reduce ambiguity by either removing irrelevant details from such illustrations (leave off axis labels on your bar chart, for example, and make it look as generic as possible) or by explicitly marking ambiguous illustrations for what they are.
* '''Clearly attribute your pictures'''. Whether a picture is a figure or an illustration, it's important to let your audience know if you did not produce it yourself. There are two reasons for this: for one, it's intellectually honest and the right thing to do. Furthermore, though, it helps your audience distinguish which pictures directly relate to your work, and which ones are more peripherally related.
* '''Use consistent symbols''' between slides. If a particular glyph, color, or figure means something specific in one slide, make sure it means the same thing in others. If you're talking about the same subject in two different slides, re-use symbols to clarify the connection between them.

== Preparation for Your Talk ==
* '''Email a day in advance''' all audience members who are supposed to be there, just to remind them. This includes (for a thesis defense, for example) your advisor, your committee members, and the additional member of the faculty who you arranged to attend. Other people may have promised they would attend; email them separately. Make sure that all your essential audience members will arrive on time.
* '''Practice tricky sections'''. Memorize, if necessary, complicated terminology, slides with a lot of text, and complicated sequences of graphical transitions. Looking at your slides rather than your audience or stumbling over your words makes you look unprofessional.
* '''Practice in the same room''' where you will give your talk. Do it a couple times, and do it earlier in the day of your talk if possible.
* If you're using Skype, '''get a lapel mic'''. The mic on your laptop may not pick up your voice well enough from across the room. Talk with [http://brown.edu/cis/services/media/ Media Technology Services] about getting a mic.
* '''Arrive early to set up''', an hour in advance if possible. Make sure your presentation is working right, that you've got all your materials on hand, that the projector works, etc.

== Presentation Style and Audience Interaction ==
* '''Ask Skyped-in audience members to mute themselves'''. People listening on their laptops often make a lot of noise without realizing it, and this can be incredibly distracting amplified over the speakers during your talk. I've seen this fuck up several defenses. The person can un-mute themselves if they need to ask a question.
* '''Pace yourself'''. Pause at the end of each section or after each significant point to implicitly or explicitly wait for questions. Count off to yourself to make sure you don't rush through this pause; subjective "presenter time" and objective "audience time" go at different rates!
* '''Use a pointer (with discretion)'''. Make sure you have a laser pointer or something equivalent (stick, telescoping pointer, finger that can reach the projection screen). When there are multiple things on a slide and you refer to them separately, indicate them both verbally and visually as you refer to them. Some people follow verbal cues better, while some are better with visual ones, so doing both covers your bases. ''Don't'' use your pointer when there's only one thing on a slide, or when you refer to multiple things as a single group; few things are more distracting than a laser pointer whizzing around needlessly. Note that '''a mouse pointer on the screen is not sufficient'''; it doesn't stand out enough against your slides and is hard to see. If using your finger, don't just point at the screen, actually tap the place you want to indicate.
* '''Check that your audience is following your talk'''. This is especially important when you have a mixed audience and a technically-difficult talk. You should have built some checkpoints into your talk; when you reach each one, ask the audience if they have any questions. If there's a specific point you need them to understand, ask them about it specifically. If they don't seem to understand, review the point and plan to go more quickly through some later section of the talk to make up the extra time.
* '''Finish on time'''. Most people find it disrespectful if a talk runs over its scheduled time limit; they have other stuff to do and don't want to choose between that and seeing your full talk (which includes Q&A afterward). It is entirely the presenter's responsibility to manage the talk in such a way that it will end on time (which is ten or fifteen minutes before the end of the meeting time, to allow for Q&A). If questions in the middle of your talk run long, that means that you have to adapt by speeding up or cutting out later sections of your talk. Talks usually start late and get interrupted a lot. It is your responsibility to plan for this. A thesis proposal, for example, is supposed to last an hour: plan for 35--40 minutes of uninterrupted talking time, knowing that you will start late, get interrupted, and have questions at the end.
* '''Avoid excessive marketing'''. Brooks: "Present to inform, not to impress; if you inform, you will impress." While it is important to avoid the question "who cares about this topic/problem?", it is also important to have your audience understand enough of the technical parts that they can draw on their collective wisdom to give advice.
* '''Show respect for audience comments'''. Note that this is different from ''having'' respect; you may have respect but still not convey it to your audience, which will alienate them from you. Here are some specific recommendations for how to convey respect:
** '''Pause after every question''' so it's clear you're thinking.
** '''Say the question back''' to the person who asked it (in your own words) to make sure you've got it right. Consider phrasing it as: "If I understand you properly, you want to know...".
** If a question isn't clear, '''say you don't understand''' and ask them to re-ask.
** '''Never cut people off''', unless you can tell the rest of the audience agrees they're rambling or wasting time, and even then, be careful. Mention that you have time constraints and offer to talk about the question offline.
** End every answer with '''"did that answer your question?"''' or something similar, even (especially?) if your answer is just, "that's a good point; I'll think about it".
** '''Answer briefly'''. Don't spend a long time waffling if a simple "yes", "no", or "I don't know" will do. Defer to the commenter when in doubt.
** '''Answer the question asked'''; don't spiral off into a discussion of something else unless it serves a point you're about to make.
** '''Be efficient with your time'''; if your answer creates a back-and-forth discussion, try to defer it to the Q&A session so you can end your talk on time.
** '''Respect ownership of ideas'''. When an audience member makes a suggestion during your talk, they may feel protective of their idea; it's a gift they're giving you, but it's important that you acknowledge that it comes from them. Some presenters try to engage with audience suggestions by connecting them to the work they've done, but this may be counterproductive. In the eyes of the person making the suggestion, this may seem like you're trying to take their idea away from them and claim it as your own, or that you don't understand the significance of what they're saying. Your first priority should be to '''acknowledge the wisdom of your audience'''. The easiest and quickest way to do this is to say something like, "that's a point I hadn't considered; thanks a lot for bringing it up. Can we talk afterward about how to incorporate it into my work?"
** Generally speaking, keep in mind: '''the audience is always right'''.

[[Category:HOWTO]][[Category:Dissemination]]

Give a talk

2012-09-23T22:42:00Z

Jadrian Miles: /* Presentation Style and Audience Interaction */ use a pointer

This page presents advice on how to give a successful talk. You will likely give many different types of talks during your time at Brown: informal elevator talks, social discussions at parties, fast-forwards during CS orientation, [[SciVis Meetings|sciviz lunch talks]] (which have their own explicit [[SciVis Meetings#Rubric for SciVis Talks|evaluation rubric]]), poster presentations at conferences, full talks at conferences, research comps proposals and defenses, thesis proposals and defenses. Each of these requires some unique understanding, but all of them share many common points. The advice below generally concerns hour-long talks, but can be adapted to any talk.

The central piece of advice, from which all the bits below may be derived, is this: '''the audience is always right'''. A talk may be about you and your work, but its real purpose is to convey ideas to your audience and to gather feedback from them. Your audience wants you to be clear, concise, efficient, and respectful. They want to feel like they understand what you're talking about, and they don't want you to waste their time or confuse them. The audience's interpretation of the talk ''is'' the reality of the talk. If you make a point but fail to convey it to the audience, you haven't really made your point. So always think about your audience when designing and refining your talk, and try to anticipate what they care about and what they'll be thinking while attending your talk.

== Talk Structure and Content ==
=== Aim for an Audience ===
* '''Know who your audience is''' and tailor your talk to this audience. Different audiences expect different talk structures, expect emphasis on different points, make different assumptions, know different background, etc. When building or editing your talk, critically ask yourself: "does my audience ''understand'' this point?" "Does my audience ''care'' about this point?" Leave out details that your audience doesn't care about (as they might serve only to confuse, distract, or take time away in your talk). Make sure to include details that your audience does care about.
** To find out who your audience will be, ask around with people who have given a similar talk at the same venue. On rare occasions, it can happen that you actually ''can't'' make a good guess about who your audience will be; for example, when you find out at the last minute that a much larger and more general audience will be attending your talk than you were told to expect. In this case, it's essential to gauge your audience's comprehension of your talk ''as you're giving it'', and adjust on the fly. See the points below about "checkpoints" and asking questions.
** ''Pro tip'': your audience for a proposal or defense is the ''faculty''. Each audience member therefore: has deep knowledge about a particular computer science subfield not necessarily related to yours, has a general knowledge of computer science, thinks about problems from a technical/algorithmic/data-oriented perspective, and is probably pretty geeky and detail-oriented. They will ask deep, probing, and potentially picky questions. Organize your talk to minimize confusion for this audience, and avoid irrelevant details that members of the audience might latch onto.
** ''Bonus pro tip'': think very explicitly about '''your goals for the talk'''. What do you want to convey to the audience? In most high-stakes talks, it's not just some fact that you worked out through your research. Other goals might include: "I want the audience to believe that I know what I'm doing." "I want my committee to let me graduate." Write these goals down and ask yourself whether the things you do and talk about in your talk serve them.
* '''Don't give the same talk to two different audiences'''. The point of a talk is to convey an idea to an audience. Each different audience has a different way of receiving ideas. This means that if you give a talk to two different audiences, it should not be the same talk, even if (to your mind) it's on the same subject.
* '''Understand the heterogeneity of your audience'''. No matter how uniform an audience might seem to be, it still contains different sub-groups. For example, for a thesis proposal presentation, your audience is composed of computer scientists, but it includes people from disciplines as diverse as natural language processing, computation theory, computational biology, and computer vision. For a presentation at an interdisciplinary conference (Vis or ISMRM, for example), your audience includes people from computer science as well as one or more application areas, and each of these communities has sub-communities (researchers vs. clinicians vs. engineers, for example).
* '''Be careful about terminology''' that means different things to different communities. Either be very explicit about the definitions of your terms, use unambiguous plain-language terms, or just drop them entirely and figure out a different way to present your point. An example list of problematic terms includes "greedy", "Monte Carlo", "solve", "optimal", "energy", "experiment", "model", "fit". If you're certain of the composition of your audience, some jargon of this sort may be acceptable, but remember that audiences are often more heterogeneous than you might think.

=== Make Them Care ===
* '''Tell them a story / put it in context'''. Your work will be most engaging when your audience understands as quickly as possible its basic context or purpose. You can achieve this by giving a simple example problem that motivates your work, an example of how someone would use your work, or an example of what your work looks like. If you can get people to care about your work in thirty seconds, put those thirty seconds at the beginning of your talk.
* '''Emphasize contributions, not design process'''. When working on a research agenda that includes multiple contributions, you may conceive of it as a sequence of experiments that you learn things from, where each experiment develops into or informs the development of the next. It's tempting to present your research in this way, to show it as a sequence of intellectual developments, but this is a mistake. Contributions are a concise and discrete way for outsiders to think about someone else's research; they provide a consistent framework in which your audience can understand the scope and impact of your work.
** If you're really itching to talk about your design process, present each research item as a separate entity and discuss intellectual connections between them as a secondary point, later in the talk.
* '''Clearly formulate a "problem statement" for each contribution'''. The truth may be messier, but for the purposes of presenting research, it's important to summarize any given contribution in terms of the problem it aims to solve, its data inputs and outputs, and how you prove your contribution. This gives your audience the understanding necessary to truly engage with your work and to think critically about it.
* '''Show concrete examples'''. Your audience will understand what you're doing better if they have a clear picture in their minds of the format of your data and problem, inputs and outputs. Unless your audience is composed of people who have the same background as you, there will be some basic point that you have to explain before getting into the specifics of your work. If you work with medical images and you're talking to a non-medical audience, show an example image. If you work with visualizations and you're talking to a non-viz audience, show some canonical examples. When reviewing results, the same thing goes: show concrete examples at the level of detail appropriate for your audience, whether illustrations, screenshots, charts, tables, or something else.
* '''Don't overstate your case'''. Explicitly establish the assumptions built into your work and the scope of your hypotheses and conclusions. Think like a scientist or mathematician and be very conservative: unless you specify the scope of your statements, it may be assumed that they apply universally, which is almost always not the case.
* '''Don't understate your case'''. Don't state your hypotheses, conclusions, or contributions with such general language that they don't actually claim anything. Be specific about the work that you did (or will do) and point out (implicitly or explicitly) its novelty and significance.
* '''Clearly establish novelty and significance'''. If your audience doesn't know the related work that you're trying to improve on, show it to them and make it clear why your work is an improvement. A comparison table is a great way to do this; greater still is a comparison table with p-values.

=== Help Them Understand ===
* '''Number your slides'''. This way, audience members who want to ask questions about specific slides can note the slide number, to make the Q&A go more smoothly.
* '''Build in checkpoints'''. A "checkpoint" is a specific time in the talk where you want to make sure your audience is caught up. For example, if concept A may be difficult for your audience to understand but is essential for understanding concept B, put a checkpoint between the explanations of the two concepts. At this checkpoint, put an overview of concept A on the slide, and plan to ask your audience if they understand it.
* '''Clearly distinguish "figures" from "illustrations"'''. Figures and illustrations are two different types of pictures. A figure is a picture that relates in a concrete and preferably quantifiable way to the work or point that you're presenting. An illustration is a generic picture that is evocative of the concept you're discussing. Trouble arises when a picture that you intend as an illustration gets misinterpreted by your audience as a figure. For example, this could happen with a bar chart. You may mean to present it as merely an example of a result that one ''might'' get, or a way that one ''might'' care to present a certain class of data, but if your audience identifies it as a figure instead, they will immediately start digging for details that will aid in its interpretation in terms of your work. This can almost fatally derail a talk. Try hard to reduce ambiguity by either removing irrelevant details from such illustrations (leave off axis labels on your bar chart, for example, and make it look as generic as possible) or by explicitly marking ambiguous illustrations for what they are.
* '''Clearly attribute your pictures'''. Whether a picture is a figure or an illustration, it's important to let your audience know if you did not produce it yourself. There are two reasons for this: for one, it's intellectually honest and the right thing to do. Furthermore, though, it helps your audience distinguish which pictures directly relate to your work, and which ones are more peripherally related.
* '''Use consistent symbols''' between slides. If a particular glyph, color, or figure means something specific in one slide, make sure it means the same thing in others. If you're talking about the same subject in two different slides, re-use symbols to clarify the connection between them.

== Preparation for Your Talk ==
* '''Email a day in advance''' all audience members who are supposed to be there, just to remind them. This includes (for a thesis defense, for example) your advisor, your committee members, and the additional member of the faculty who you arranged to attend. Other people may have promised they would attend; email them separately. Make sure that all your essential audience members will arrive on time.
* '''Practice tricky sections'''. Memorize, if necessary, complicated terminology, slides with a lot of text, and complicated sequences of graphical transitions. Looking at your slides rather than your audience or stumbling over your words makes you look unprofessional.
* '''Practice in the same room''' where you will give your talk. Do it a couple times, and do it earlier in the day of your talk if possible.
* If you're using Skype, '''get a lapel mic'''. The mic on your laptop may not pick up your voice well enough from across the room. Talk with [http://brown.edu/cis/services/media/ Media Technology Services] about getting a mic.
* '''Arrive early to set up''', an hour in advance if possible. Make sure your presentation is working right, that you've got all your materials on hand, that the projector works, etc.

== Presentation Style and Audience Interaction ==
* '''Ask Skyped-in audience members to mute themselves'''. People listening on their laptops often make a lot of noise without realizing it, and this can be incredibly distracting amplified over the speakers during your talk. I've seen this fuck up several defenses. The person can un-mute themselves if they need to ask a question.
* '''Pace yourself'''. Pause at the end of each section or after each significant point to implicitly or explicitly wait for questions. Count off to yourself to make sure you don't rush through this pause; subjective "presenter time" and objective "audience time" go at different rates!
* '''Use a pointer (with discretion)'''. Make sure you have a laser pointer or something equivalent (stick, telescoping pointer, finger that can reach the projection screen). When there are multiple things on a slide and you refer to them separately, indicate them both verbally and visually as you refer to them. Some people follow verbal cues better, while some are better with visual ones, so doing both covers your bases. ''Don't'' use your pointer when there's only one thing on a slide, or when you refer to multiple things as a single group; few things are more distracting than a laser pointer whizzing around needlessly. Note that '''a mouse pointer on the screen is not sufficient'''; it doesn't stand out enough against your slides and is hard to see.
* '''Check that your audience is following your talk'''. This is especially important when you have a mixed audience and a technically-difficult talk. You should have built some checkpoints into your talk; when you reach each one, ask the audience if they have any questions. If there's a specific point you need them to understand, ask them about it specifically. If they don't seem to understand, review the point and plan to go more quickly through some later section of the talk to make up the extra time.
* '''Finish on time'''. Most people find it disrespectful if a talk runs over its scheduled time limit; they have other stuff to do and don't want to choose between that and seeing your full talk (which includes Q&A afterward). It is entirely the presenter's responsibility to manage the talk in such a way that it will end on time (which is ten or fifteen minutes before the end of the meeting time, to allow for Q&A). If questions in the middle of your talk run long, that means that you have to adapt by speeding up or cutting out later sections of your talk. Talks usually start late and get interrupted a lot. It is your responsibility to plan for this. A thesis proposal, for example, is supposed to last an hour: plan for 35--40 minutes of uninterrupted talking time, knowing that you will start late, get interrupted, and have questions at the end.
* '''Avoid excessive marketing'''. Brooks: "Present to inform, not to impress; if you inform, you will impress." While it is important to avoid the question "who cares about this topic/problem?", it is also important to have your audience understand enough of the technical parts that they can draw on their collective wisdom to give advice.
* '''Show respect for audience comments'''. Note that this is different from ''having'' respect; you may have respect but still not convey it to your audience, which will alienate them from you. Here are some specific recommendations for how to convey respect:
** '''Pause after every question''' so it's clear you're thinking.
** '''Say the question back''' to the person who asked it (in your own words) to make sure you've got it right. Consider phrasing it as: "If I understand you properly, you want to know...".
** If a question isn't clear, '''say you don't understand''' and ask them to re-ask.
** '''Never cut people off''', unless you can tell the rest of the audience agrees they're rambling or wasting time, and even then, be careful. Mention that you have time constraints and offer to talk about the question offline.
** End every answer with '''"did that answer your question?"''' or something similar, even (especially?) if your answer is just, "that's a good point; I'll think about it".
** '''Answer briefly'''. Don't spend a long time waffling if a simple "yes", "no", or "I don't know" will do. Defer to the commenter when in doubt.
** '''Answer the question asked'''; don't spiral off into a discussion of something else unless it serves a point you're about to make.
** '''Be efficient with your time'''; if your answer creates a back-and-forth discussion, try to defer it to the Q&A session so you can end your talk on time.
** '''Respect ownership of ideas'''. When an audience member makes a suggestion during your talk, they may feel protective of their idea; it's a gift they're giving you, but it's important that you acknowledge that it comes from them. Some presenters try to engage with audience suggestions by connecting them to the work they've done, but this may be counterproductive. In the eyes of the person making the suggestion, this may seem like you're trying to take their idea away from them and claim it as your own, or that you don't understand the significance of what they're saying. Your first priority should be to '''acknowledge the wisdom of your audience'''. The easiest and quickest way to do this is to say something like, "that's a point I hadn't considered; thanks a lot for bringing it up. Can we talk afterward about how to incorporate it into my work?"
** Generally speaking, keep in mind: '''the audience is always right'''.

[[Category:HOWTO]][[Category:Dissemination]]

User:Jadrian Miles

2012-09-19T14:31:04Z

Jadrian Miles: Undo revision 6215 by Jadrian Miles (talk)

I started my PhD in CS at Brown in Fall 2006. I work on data processing, measurement, and model reconstruction from [[diffusion MRI]] of the brain.

You can find me elsewhere online:
* [http://cs.brown.edu/~jadrian CS department page]
* [http://vis.cs.brown.edu/organization/people/jadrian.html Visweb profile]
* [http://www.google.com/search?q=jadrian+miles Other places]

There are a number of directories related to me on the CS filesystem, all of which are linked from file:///map/gfx0/users/jadrian

==== Personal Documents ====
* '''Planning Documents'''
** [[/OKRs]] ([[/OKRs/Summer 2012|2012Sum]]) ([[/OKRs/Spring 2012|2012S]]) ([[/OKRs/Fall 2011|2011F]])
** [[:Image:Jadrian Miles PhD Proposal rev3 2010-09-10.pdf|Thesis proposal (v3, 2010-09-10)]] ([[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|v2, 2009-10-15]]) ([[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|v1, 2009-06-22]])
** [[/Paper list]]
** [[/End-of-PhD cleanup taks]]
* '''Project Notes'''
** [[/Chi-squared clustering]]
** [[/Triangle toy problem]]
** [[/vis2011 tractography statistics paper]]
** [[/Thesis manifesto: probabilistic worldview]]
* '''Archive'''
** [[/PhD Plan]]
** [[/Thesis proposal feedback]]
** [[/Research Projects]]
** [[/Diffusion simulation]]
** [[/Streamline clustering]]
** [[/Cluster slicing notes]]

==== Draft pages / notes ====
* [[/Theory Conference Deadlines]]
* [[/Plan your PhD]]
* [[/Diffusion MRI techniques]]
* [[/BB's dollarg]]
* [[/Eclipse]]
* [[/sandbox]]

==== Nifty code snippets ====
* Generate a random filename from the command line: <pre>set tmpfile=/tmp/`head -q -c 8 /proc/sys/kernel/random/uuid`</pre>
* Convert stdin to lowercase on stdout: <pre>tr '[A-Z]' '[a-z]'</pre>
* Rename files into consecutive zero-padded integers in <tt>bash</tt>: <pre>let i=0; for f in *.JPG; do mv $f `printf "%04d" $i`.jpg; let i++; done</pre>
* Test for host availability in <tt>tcsh</tt> (for loop demo; see [http://www.cyberciti.biz/faq/bash-for-loop/ here] for bash example):
<pre style="margin-left:1.5em">
foreach h ( `cat hostlist` )
ssh $h uname -n
end
</pre>
* Update a directory with stuff that exists in a CVS repository but not in the directory:
*;<pre>cvs update -d</pre>
* Concatenate PDFs (more at [http://web.archive.org/web/20090223000710/http://ansuz.sooke.bc.ca/software/pdf-append.php? the original source]; even more [http://nixtricks.wordpress.com/2009/09/01/cli-combine-or-remove-pages-from-a-pdf-document-using-ghostscript/ elsewhere])
*;<pre>gs -q -sPAPERSIZE=letter -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=out.pdf in1.pdf in2.pdf in3.pdf ...</pre>
* Recache TeX search paths:
*;<pre>sudo mktexlsr</pre>
* Perceptually uniform random coloring in Matlab
<pre style="margin-left:1.5em">
C = makecform('lab2srgb');
plot3(X,Y,Z,'Color', applycform([50+rand*50, -100+rand*200, -100+rand*200], C));
</pre>
* Recursively download a website using wget (see [http://www.editcorp.com/Personal/Lars_Appel/wget/wget_2.html#SEC11 the man page] for more) <pre>wget -r -np -nH http://www.site.com/subdir</pre>

==== Bookmarks ====
* [http://when2meet.com when2meet.com] --- lightweight meeting scheduling thingie

==== Tutorials ====
* [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance.htm Covariance] and [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance_matrix.htm covariance matrix]
* [http://www.tommangan.us/Tensors.pdf Tensors]
* Quaternions
* Levenberg-Marquardt / Lagrange Multipliers

==== Miscellaneous notes ====
* High b sensitizes to short length scale (Assaf & Cohen 1998, 2000).
* The cingulum bundle looks like a long, skinny tube (that wraps around the top and back of the CC) in a gross segmentation, and fibers run along the long axis of this tube for most of this length. Their projections into the GM, though, are actually along the side of the tube, on mid-sagittal gyri. This is a really weird shape when it comes to inferring fiber paths from the bundle shape, so it should be a smoke test for any proposed system.
* Sculpture might be a good choice for the second outside minor course. 3D reasoning, malleable shapes...

User:Jadrian Miles

2012-09-19T14:26:18Z

Jadrian Miles:

I started my PhD in CS at Brown in Fall 2006. I work on data processing, measurement, and model reconstruction from [[diffusion MRI]] of the brain.

You can find me elsewhere online:
* [http://cs.brown.edu/~jadrian CS department page]
* [http://vis.cs.brown.edu/organization/people/jadrian.html Visweb profile]
* [http://www.google.com/search?q=jadrian+miles Other places]

There are a number of directories related to me on the CS filesystem, all of which are linked from file:///map/gfx0/users/jadrian

==== Personal Documents ====
* '''Planning Documents'''
** [[/OKRs]] ([[/OKRs/Summer 2012|2012Sum]]) ([[/OKRs/Spring 2012|2012S]]) ([[/OKRs/Fall 2011|2011F]])
** [[:Image:Jadrian Miles PhD Proposal rev3 2010-09-10.pdf|Thesis proposal (v3, 2010-09-10)]] ([[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|v2, 2009-10-15]]) ([[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|v1, 2009-06-22]])
** [[/Paper list]]
** [[/End-of-PhD cleanup taks]]
** [[/Job opportunities]]
* '''Project Notes'''
** [[/Chi-squared clustering]]
** [[/Triangle toy problem]]
** [[/vis2011 tractography statistics paper]]
** [[/Thesis manifesto: probabilistic worldview]]
* '''Archive'''
** [[/PhD Plan]]
** [[/Thesis proposal feedback]]
** [[/Research Projects]]
** [[/Diffusion simulation]]
** [[/Streamline clustering]]
** [[/Cluster slicing notes]]

==== Draft pages / notes ====
* [[/Theory Conference Deadlines]]
* [[/Plan your PhD]]
* [[/Diffusion MRI techniques]]
* [[/BB's dollarg]]
* [[/Eclipse]]
* [[/sandbox]]

==== Nifty code snippets ====
* Generate a random filename from the command line: <pre>set tmpfile=/tmp/`head -q -c 8 /proc/sys/kernel/random/uuid`</pre>
* Convert stdin to lowercase on stdout: <pre>tr '[A-Z]' '[a-z]'</pre>
* Rename files into consecutive zero-padded integers in <tt>bash</tt>: <pre>let i=0; for f in *.JPG; do mv $f `printf "%04d" $i`.jpg; let i++; done</pre>
* Test for host availability in <tt>tcsh</tt> (for loop demo; see [http://www.cyberciti.biz/faq/bash-for-loop/ here] for bash example):
<pre style="margin-left:1.5em">
foreach h ( `cat hostlist` )
ssh $h uname -n
end
</pre>
* Update a directory with stuff that exists in a CVS repository but not in the directory:
*;<pre>cvs update -d</pre>
* Concatenate PDFs (more at [http://web.archive.org/web/20090223000710/http://ansuz.sooke.bc.ca/software/pdf-append.php? the original source]; even more [http://nixtricks.wordpress.com/2009/09/01/cli-combine-or-remove-pages-from-a-pdf-document-using-ghostscript/ elsewhere])
*;<pre>gs -q -sPAPERSIZE=letter -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=out.pdf in1.pdf in2.pdf in3.pdf ...</pre>
* Recache TeX search paths:
*;<pre>sudo mktexlsr</pre>
* Perceptually uniform random coloring in Matlab
<pre style="margin-left:1.5em">
C = makecform('lab2srgb');
plot3(X,Y,Z,'Color', applycform([50+rand*50, -100+rand*200, -100+rand*200], C));
</pre>
* Recursively download a website using wget (see [http://www.editcorp.com/Personal/Lars_Appel/wget/wget_2.html#SEC11 the man page] for more) <pre>wget -r -np -nH http://www.site.com/subdir</pre>

==== Bookmarks ====
* [http://when2meet.com when2meet.com] --- lightweight meeting scheduling thingie

==== Tutorials ====
* [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance.htm Covariance] and [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_covariance_matrix.htm covariance matrix]
* [http://www.tommangan.us/Tensors.pdf Tensors]
* Quaternions
* Levenberg-Marquardt / Lagrange Multipliers

==== Miscellaneous notes ====
* High b sensitizes to short length scale (Assaf & Cohen 1998, 2000).
* The cingulum bundle looks like a long, skinny tube (that wraps around the top and back of the CC) in a gross segmentation, and fibers run along the long axis of this tube for most of this length. Their projections into the GM, though, are actually along the side of the tube, on mid-sagittal gyri. This is a really weird shape when it comes to inferring fiber paths from the bundle shape, so it should be a smoke test for any proposed system.
* Sculpture might be a good choice for the second outside minor course. 3D reasoning, malleable shapes...

User:Jadrian Miles/OKRs

2012-09-06T15:59:13Z

Jadrian Miles: Beginning OKRs for fall 2012

Today's Date: '''{{CURRENTMONTH}}/{{CURRENTDAY2}}'''

* Meta-objective: Be ready to defend by March.
** Objective: Write a dissertation that covers and synthesizes the work I've done.
** Objective: Salvage something dissertation-worthy from the tract-noise experiments.
** Objective: Demonstrate novelty & significance of the "blockhead" method in the dissertation.

User:Jadrian Miles/OKRs/Summer 2012

2012-09-06T15:53:13Z

Jadrian Miles: Summer OKRs, plus assessments

* Meta-objective: make measurable progress toward the dissertation.
** Key result: {{red|TODO}}
* Meta-objective: concretely demonstrate the success of the real-problem technique.
** Demonstrate (by pictures) specific challenging regions in which the multi-scale approach reconstructs structures better than two competitors.
** Demonstrate (numerically) that image reconstruction, as measured by chi-squared goodness-of-fit on real data, is better than two competitors.
** Demonstrate (in prose, or maybe with a quick user study) that selection tasks for specific brain structures are easier and more precise than with ROI+tractography methods.
*** {{yellow|The real problem as originally formulated has been abandoned as impractical in the timeframe I have.}}
* Objective: Write and submit the tract noise paper in a timely manner.
** Key result: Experiments 1 & 2, plus analysis and figures, are finished by '''06/19'''.
** Key result: Experiment 3 is finished within two weeks of the IIT data posting online.
** Key result: Complete first draft to dhl within a week of finishing experiment 3.
** Key result: Paper submitted to MRM by end of August.
*** {{red|Later experiments were delayed, and finally the results were negative. Considering rebooting for the fall.}}
* Objective: Design, implement, and evaluate a curve-bundle model.
** Key result: Bundle model initialized from existing cluster data by '''06/22'''.
** Key result: Bundle joining and splitting implemented by '''06/29'''.
*** {{yellow|This line of research has been abandoned as impractical in the timeframe I have.}}

User talk:Connor Gramazio

2012-09-06T13:39:46Z

Jadrian Miles: Welcome!

'''Welcome to ''VrlWiki''!'''
We hope you will contribute much and well.
You will probably want to read the [[Help:Contents|help pages]].
Again, welcome and have fun! [[User:Jadrian Miles|Jadrian Miles]] 09:39, 6 September 2012 (EDT)

User:Connor Gramazio

2012-09-06T13:39:46Z

Jadrian Miles: Creating user page with biography of new user.