View source for Diffusion MRI

''Diffusion-weighted magnetic resonance imaging'' ('''DW-MRI''') is a radiological technique that measures water diffusion in living tissue in order to infer microstructural details of fibrous textured tissues like brain [[w:white matter|white matter]].  The information that comes from a DW-MRI scan sequence generally requires extensive processing before it is useful for brain scientists --- see the article on [[diffusion MRI techniques]] for more details.  Our research group collaborates with scientists around the world to help make medical discoveries while developing novel techniques to process, quantify, and visualize diffusion MRI data.

You may also want to check the [[/Glossary|diffusion MRI glossary]] page to learn some jargon, or the [[brain anatomy]] page.

== Neuroscience Collaborations ==
The following is a table of all the projects on which we're collaborating, the data we've received from our collaborators, information about the data, and our progress in processing them.

Entries in the "Dataset Date Received" column may include a "[more]" link.  This drops down more detail, including the path to the data and additional notes.  Relative paths start at the directory [file:///data/graphics/mri/ <tt>/data/graphics/mri/</tt>].

In the "Status" column, the rule of thumb is to only mark a particular stage completed if it's completed for all scans (usually corresponding to patients) in the dataset.  Sometimes a step will be marked complete if it's known to work for all scans but has not been completed on a minority of them, but this practice is discouraged.

In the "Resolution" and "Voxel Size" columns, dimensions are ordered XxYxZ.

In the "Orientation" columns, "L" stands for "patient's left".  "R" stands for "patient's right".  "A" stands for "anterior" (front), "P" for "posterior" (back), "I" for "inferior" (bottom), and "S" for "superior" (top).  See the [[w:Anatomical terms of location#Medical (human) directional terms|wikipedia page on anatomical coordinate systems]] for more information.  The default orientation in the table below is "RL", "AP", and "IS"; if they are in the opposite order it indicates a [[Diagnose tensor orientation problems|direction flip]].

Note that this "default orientation" is non-standard; NIfTI, Talairach, and MNI coordinate systems all specify that X increases L-to-R; Y, P-to-A; and Z, I-to-S.  The default orientation is still a right-handed coordinate system (thank goodness), but it's a little wonky and may cause problems with certain software.  Check out [http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q14 the NIfTI FAQ on orientation] and [http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm Graham Wideman's helpful tutorial] for more information.  There's the chance that all of the orientation tags in this table have systematic errors, so a wholesale review of them might be worthwhile at some point.  For the time being, take them with a grain of salt and double-check if it's important.

=== Collaboration Table ===

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=================================== WANNA MAKE A NEW ENTRY IN THE TABLE? ==================================
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MediaWiki's table syntax is pretty gross, and this table is a complicated one.  Below is a a template for creating an entirely new project entry; anything where you're adding content to an existing project is probably worth just talking to Jadrian about, as it involves nasty things like "rowspan".  If you have a healthy familiarity with HTML table syntax, you'll probably be fine just studying what's already in the table.

{{yes}} or {{Y}} gives you a green cell with a Y in it; {{no}} or {{N}} gives you a red cell with an N in it; {{?}} gives you a grey cell with a ? in it.

A new project entry looks like this:

------- BEGIN NEW ENTRY TEMPLATE (don't include this line) -------
|-
| {{Hl2}} | <PROJECT_NAME>
| <LOCATION>
| <COLLABORATORS>
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = <DATE_RECEIVED>
| content = <small><code><PATH_TO_DATA></code></small><NOTES_IF_ANY>
}}
| <COLLECTED_BY_COLLABORATOR?>
| <UPLOADED_TO_FTP_BY_COLLABORATOR?>
| <DOWNLOADED_FROM_FTP?>
| <FILED_IN_$G/DATA/DIFFUSION?>
| <CONVERTED_TO_MRIIMAGE?>
| <TENSORS_FIT?>
| <TUBES_GENERATED?>
| <BRAINAPP_WORKS?>
| <SCANNER_FIELD_STRENGTH>
| <SCANNER_MANUFACTURER>
| <FILE_TYPE>
| <NUMBER_OF_SCANS>
| <RESOLUTION_IN_VOXELS>
| <NUMBER_OF_DWIS>
| <VOXEL_SIZE_IN_MM>
| <DWI_-X>  || <DWI_+X>  || <DWI_-Y>  || <DWI_+Y>  || <DWI_-Z>  || <DWI_+Z>
| <BVEC_-X> || <BVEC_+X> || <BVEC_-Y> || <BVEC_+Y> || <BVEC_-Z> || <BVEC_+Z>
------- END NEW ENTRY TEMPLATE (don't include this line) -------

You may want to replace the whole last line with '| colspan="6" {{?}}' if you don't know the orientation.

Okay, that's all I've got.  If you need help, ask Jadrian.  Below this next line is where the table starts.
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{| {{Prettytable}}
|-
! {{Hl2}} rowspan="2" | Project
! {{Hl2}} rowspan="2" | Location
! {{Hl2}} rowspan="2" | Collaborators
! {{Hl2}} rowspan="2" | Dataset Date Received
! {{Hl2}} colspan="8" | Status
! {{Hl2}} colspan="2" | Scanner
! {{Hl2}} rowspan="2" | Format
! {{Hl2}} rowspan="2" | &#035; Scans
! {{Hl2}} rowspan="2" | Resolution (voxels)
! {{Hl2}} rowspan="2" | &#035; DWIs
! {{Hl2}} rowspan="2" | Voxel Size (mm)
! {{Hl2}} colspan="6" | DWI Orientation
! {{Hl2}} colspan="6" | bvec Orientation
|- 
! {{Hl2}} | <abbr title="Scans collected by collaborator?">C</abbr>
! {{Hl2}} | <abbr title="Scans uploaded to our FTP by collaborator?">U</abbr>
! {{Hl2}} | <abbr title="Scans downloaded from our FTP?">D</abbr>
! {{Hl2}} | <abbr title="Scans filed in $G/data/diffusion?">F</abbr>
! {{Hl2}} | <abbr title="DWIs converted to MriImage?">M</abbr>
! {{Hl2}} | <abbr title="Tensors fit?">F</abbr>
! {{Hl2}} | <abbr title="Tubes generated?">T</abbr>
! {{Hl2}} | <abbr title="Works in Brainapp?">B</abbr>
! {{Hl2}} | <abbr title="Field strength">F</abbr>
! {{Hl2}} | <abbr title="Brand/Manufacturer">B</abbr>
! {{Hl2}} | -X
! {{Hl2}} | +X
! {{Hl2}} | -Y
! {{Hl2}} | +Y
! {{Hl2}} | -Z
! {{Hl2}} | +Z
! {{Hl2}} | -X
! {{Hl2}} | +X
! {{Hl2}} | -Y
! {{Hl2}} | +Y
! {{Hl2}} | -Z
! {{Hl2}} | +Z
|-
| {{Hl2}} rowspan=2 | Cognitive Aging
| rowspan=2 | St. Louis
| rowspan=2 | Rob&nbsp;Paul&nbsp;([[Wikipedia:UMSL|UMSL]]),<br/>Tom&nbsp;Conturo&nbsp;([[Wikipedia:WUSTL|WUSTL]])
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-07-20
| content = <small><code>st_louis/pilot_data.2008.07.20</code></small>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| {{?}}
| [[Analyze]] .img + [[Interfile]] .ifh header
| 1
| 83x110x64
| 36
| 2.0x2.0x2.0
| R || L || {{no|P}} || {{no|A}} || I || S
| R || L || A || P || I || S
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2010-07-09
| content = <small><code>st_louis/aging_brains.2010.07.09</code></small>
}}
| {{yes}}
| {{n}}
| {{n}}
| {{n}}
| {{n}}
| {{n}}
| {{n}}
| {{n}}
| {{?}}
| {{?}}
| [[Analyze]] .hdr/.img + [[Interfile]] .ifh header (supplementary)
| 81
| 83x110x64
| 64 for d1 scans; 72 for d2 scans
| 2.0x2.0x2.0
| R || L || {{no|P}} || {{no|A}} || I || S
| R || L || A || P || I || S
|-
| {{Hl2}} rowspan="2" | [[Fibers at Risk]]
| Colorado
| Jack Simon
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-08-28
| content = Longitudinal data collected a long while ago, mailed to us on DVD.
}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| 1.5T
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| Portland
| Jack&nbsp;Simon&nbsp;([[wikipedia:VA Hospital|VA]]),<br/>Bill&nbsp;Rooney&nbsp;([[wikipedia:OHSU|OHSU]]&nbsp;<abbr title="Advanced Imaging Research Center">AIRC</abbr>)
| 
| 
| 
| 
| 
| 
| 
| 
| 
| 7T
| GE
| 
| 
| 
| 
| 
| colspan="6" | 
| colspan="6" | 
|-
| {{Hl2}} rowspan="4" | HIV
| Memorial Hospital
| rowspan="4" | Steve&nbsp;Correia,<br/>Ron&nbsp;Cohen
| {{?}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| 1.5T
| Siemens
| [[DICOM]]
| {{?}}
| 256x256x90
| {{?}}
| 0.8477x0.8477x1.667
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| rowspan="3" | Brown Life Sci
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2007-11-30
| content = <small><code>brown3t/302CK.2007.11.30</code></small>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| rowspan="3" | 3T
| rowspan="3" | Siemens
| [[DICOM]]
| 1
| 256x256x180
| 74
| .8828x.8828x.7
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-07-21
| content = <small><code>brown3t/cohen_hiv_study.2007.02.07</code></small>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| [[NIfTI]]
| 13
| 128x128x70
| 74
| 1.76562x1.76562x1.8
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-10-09
| content = <small><code>brown3t/cohen_hiv_study_registered.2007.02.07</code></small>
}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| [[NIfTI]]
| 8
| 128x128x70
| 74
| 1.76562x1.76562x1.8
| R || L || A || P || I || S
| {{no|L}} || {{no|R}} || A || P || I || S
|-
| {{Hl2}} | Kids
| Hasbro / Coro
| Daniel Dickstein
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2010-01-13
| content = <small><code>hasbro/test_data.2010.01.13</code></small>
}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{n}}
| {{n}}
| {{n}}
| {{n}}
| {{?}}
| {{?}}
| [[NIfTI]]
| 4
| 128x128x70
| 65
| 1.765625x1.765625x1.8
| R || L || A || P || I || S
| R || L || A || P || I || S
|-
| {{Hl2}} | Macaque
| Brown
| John&nbsp;Donoghue, Kaivon&nbsp;Paroo
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2010-02-09
| content = <small><code>brown3t/donoghue_macaque.2010.01.21</code></small>
}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{n}}
| {{n}}
| {{n}}
| {{n}}
| 3T
| Siemens
| [[DICOM]]
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| colspan=6 {{?}}
| colspan=6 {{?}}
|-
| {{Hl2}} | Macaque Histology
| Caltech
| Jason Kaufman
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-05-21
| content = <small><code>caltech/macaque.2008.05.21</code></small>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| Bruker
| [[Analyze]]
| 1
| 98x110x130
| 36
| 0.6x0.6x0.6
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{Hl2}} rowspan="4" | SA HIV
| rowspan="4" | Cape Town
| rowspan="4" | Rob&nbsp;Paul&nbsp;(PI), Bruce&nbsp;Spottiswoode, Paul&nbsp;Carey, John&nbsp;Joska
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2007-10-22
| content = <small><code>south_africa/normal.2007.10.22</code></small>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| Siemens
| [[DICOM#Mosaic|DICOM Mosaic]]
| 1
| 127x128x70
| 40
| 1.71875x1.71875x1.7
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-05-09
| content = <small><code>south_africa/normal.2008.05.06.average1</code></small><br/><small><code>south_africa/normal.2008.05.06.average2</code></small><br/><small><code>south_africa/hiv.2008.05.09</code></small>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| Siemens
| [[DICOM#Mosaic|DICOM Mosaic]]
| 3
| 127x127x75
| 66
| 1.71875x1.71875x1.7
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 85ex;
| header = 2008-07-24
| content = <small><code>south_africa/hiv_positive_apathy_negative_15patients.2008.07.24</code></small>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| Siemens
| 4-D [[NIfTI]]
| 15
| 128x128x75
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 9ex; | contentcss = font-size: 90%; width: 25ex;
| header = 65
| content = For each patient, there are 5 acquisitions in 13 directions each, all registered to each other.  Each acquisition is a separate 4-D [[NIfTI]] file.
}}
| 1.875x1.875x1.9
| R || L || A || P || I || S
| R || L || A || P || I || S
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 85ex;
| header = 2009-11-27
| content = <small><code>south_africa/rp_study.2009.11.27</code></small>
}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| {{?}}
| [[DICOM#Mosaic|DICOM Mosaic]]
| 30
| 128x128x70
| 33
| 1.71875x1.71875x1.7
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{Hl2}} rowspan="4" | [[Tumors]]
| rowspan="4" | Edinburgh
| rowspan="4" | Mark Bastin
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2007-11-06
| content = <small><code>edinburgh/tumor.2007.11.06</code></small>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| 1.5T
| GE
| [[DICOM#Tar|DICOM tarball]]
| 1
| 128x128x72
| 71
| 2.0x2.0x2.0
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-07-24
| content = <small><code>edinburgh/tumor_pilot.2008.07.24</code></small>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{some}}
| {{some}}
| {{some}}
| 1.5T
| GE
| [[DICOM#Tar|DICOM tarball]]
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 9ex; | contentcss = font-size: 90%; width: 25ex;
| header = 29
| content = 1 scan each of 5 tumor patients, plus 3 scans each of 8 healthy volunteers.
}}
| 128x128x72
| 71
| 2.0x2.0x2.0
| R || L || A || P || I || S
| R || L || {{no|P}} || {{no|A}} || I || S
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2009-11-23
| content = <small><code>edinburgh/tumor_fullstudy.2009.11.23</code></small>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{some}}
| {{some}}
| {{some}}
| {{some}}
| 1.5T
| GE
| [[DICOM#Tar|DICOM tarball]]
| 17
| 128x128x72
| 71
| 2.0x2.0x2.0
| R || L || A || P || I || S
| R || L || {{no|P}} || {{no|A}} || I || S
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2009-12-21
| content = <small><code>edinburgh/normals.2009.12.21</code></small>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| 1.5T
| GE
| [[DICOM#Tar|DICOM tarball]]
| 36
| 128x128x72
| 71
| 2.0x2.0x2.0
| R || L || A || P || I || S
| R || L || {{no|P}} || {{no|A}} || I || S
|}

=== Brown Protocol Compatibility Study ===

The 3T scanner at Brown has changed its configuration several times, necessitating a study to determine whether data from these different configurations are compatible.  Please see the page [[/Brown Protocol Compatibility Study]] for details.

== Software ==
The principal pieces of software we use for research now are:
* [[Diffusion Processing Pipeline]] --- a series of small programs that turns data we get from collaborators into tensor models, scalar measures, tractograms, etc.
* [[Brainapp]] --- a GUI program for viewing tractograms and computing scalar statistics on them.
* <code>$G/bin/mriatlas</code> --- generates a PDF of slices of [[MRIimage]] files.
* [[Diffusion MRI Matlab Scripts]] --- Matlab scripts to read, write, view, and manipulate MRI data (especially in [[MRIimage]] format)

You may also be interested in the exhaustive list of [[In-House Diffusion MRI Software|diffusion MRI software we've developed in-house]], or that of [[3rd Party Diffusion MRI Software|3rd-party software]].

== File Formats ==
{| {{Prettytable | width = 40%}}
|-
! {{Hl2}} | Format
! {{Hl2}} | Extension
|-
| [[DICOM]]
| <tt>.ima</tt>; <tt>.dcm</tt>
|- 
| [[Analyze]]
| <tt>.hdr</tt> / <tt>.img</tt>
|-
| [[NIfTI]]
| <tt>.nii</tt>; <tt>.nii.gz</tt>; <tt>.hdr</tt> / <tt>.img</tt>
|-
| [[Interfile]]
| <tt>.ifh</tt> / <tt>.img</tt>; <tt>.i33</tt> / <tt>.h33</tt>
|-
| [[MRIimage]]
| ''none''
|}

== HOWTOs ==
* [[Set up your environment for diffusion MRI processing]]
* [[Run the diffusion processing pipeline at low resolution]]
* [[Diagnose tensor orientation problems]]
* [[Compute apparent diffusion coefficient]]

== See Also ==
* [[/Introductory Reading List|Introductory Reading List]] --- a minimal guide of good references for understanding the background of this project
* [[Diffusion Processing Pipeline]] --- a series of small programs that turns data we get from collaborators into tensor models, scalar measures, tractograms, etc.
* [[Brainapp]] --- a GUI program for viewing tractograms and computing scalar statistics on them.
* [[Diffusion MRI Matlab Scripts]] --- Matlab scripts to read, write, view, and manipulate MRI data (especially in [[MRIimage]] format)
* [[Diffusion MRI techniques]] --- technical information about the diffusion MRI process
* [[Brain anatomy]]
* [[/Glossary|Diffusion MRI glossary]]
* [[Work With Histology Data]]
* [[Diffusion MRI Design Notes]]
* [[Brain Networks]]
* [[Neuroimaging Systems]]

[[Category:Projects]][[Category:Diffusion MRI]]