Diffusion MRI: Difference between revisions

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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 "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 "Orientation" column, "L" stands for "left side of patient from an anterior view", or "patient's right".  "R" stands for "right side of patient from an anterior view", or "patient's left".  "A" stands for "anterior", "P" for "posterior", "I" for "inferior", and "S" for "superior".  See the [[w:Anatomical terms of location#Medical (human) directional terms|wikipedia page on anatomical coordinate systems]] for more information.  Ordinarily you will see these pairs in order as "LR", "AP", and "IS"; if they are in the opposite order it indicates a [[Diagnose tensor orientation problems|direction flip]].
In the "Resolution" and "Voxel Size" columns, dimensions are ordered XxYxZ.


In the "Orientation" column, "L" stands for "left side of patient from an anterior view", or "patient's right".  "R" stands for "right side of patient from an anterior view", or "patient's left".  "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.  Ordinarily you will see these pairs in order as "LR", "AP", and "IS"; if they are in the opposite order it indicates a [[Diagnose tensor orientation problems|direction flip]].
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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 = <code><PATH_TO_DATA></code>
}}
| <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>
| <-X_ORIENTATION> || <+X_ORIENTATION> || <-Y_ORIENTATION> || <+Y_ORIENTATION> || <-Z_ORIENTATION> || <+Z_ORIENTATION>
------- 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.
-->
{| {{Prettytable}}
{| {{Prettytable}}
|-
|-

Revision as of 23:52, 7 November 2008

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.

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" column, "L" stands for "left side of patient from an anterior view", or "patient's right". "R" stands for "right side of patient from an anterior view", or "patient's left". "A" stands for "anterior" (front), "P" for "posterior" (back), "I" for "inferior" (bottom), and "S" for "superior" (top). See the wikipedia page on anatomical coordinate systems for more information. Ordinarily you will see these pairs in order as "LR", "AP", and "IS"; if they are in the opposite order it indicates a direction flip.

Project Location Collaborators Dataset Date Received / Path Status Scanner Format # Scans Resolution (voxels) # DWIs Voxel Size (mm) Orientation
C U D F M F T B F B -X +X -Y +Y -Z +Z
Cognitive Aging St. Louis Rob Paul (UMSL),
Tom Conturo (WUSTL)
2008-07-20
Y Y Y Y N N N N ? ? Interfile 1 83x110x64 36 2.0x2.0x2.0 ?
Fibers at Risk Colorado Jack Simon ? Y Y N N N N N N 1.5T ? ? ? ? ? ? ?
Portland Jack Simon (VA),
Bill Rooney (OHSU AIRC) 		? N N N N N N N N 7T GE ? ? ? ? ? ?
HIV Memorial Hospital Steve Correia,
Ron Cohen 		? Y Y Y N N N N N 1.5T ? DICOM ? 256x256x90 ? 0.8477x0.8477x1.667 ?
Brown Life Sci
2007-11-30
Y Y Y Y Y N N N 3T ? ? 1 ? ? ? ?
2008-07-21
Y Y Y Y Y Y Y Y NIfTI 13 128x128x70 74 1.76562x1.76562x1.8 ?
2008-10-09
Y Y Y Y N N N N NIfTI 8 128x128x70 74 1.76562x1.76562x1.8 R L A P I S
Macaques Caltech Jason Kaufman
2008-05-21
Y Y Y Y Y Y Y Y ? Bruker DICOM? 1 98x110x130 36 0.6x0.6x0.6 ?
SA HIV Cape Town Bruce Spottiswoode
2007.10.22
Y Y Y Y Y Y Y Y ? ? DICOM Mosaic 1 127x128x70 40 1.71875x1.71875x1.7 ?
2008.05.09
Y Y Y Y N N N N ? ? DICOM Mosaic 3 127x127x75 66 1.71875x1.71875x1.7 ?
2008.07.24
Y Y Y Y N N N N ? ? ? 15 ? ? ? ?
Tumors Edinburgh Mark Bastin
2007-11-06
Y Y Y Y N N N N ? ? ? 1 ? ? ? ?
2008-07-24
Y Y Y Y N N N N ? ? ? 3 ? ? ? ?

Software

See also the list of 3rd-party software.

File Formats

Format Extension
DICOM .ima; .dcm
DICOM Mosaic .ima; .dcm
Analyze .hdr / .img
NIfTI .nii; .nii.gz; .hdr / .img
Interfile .ifh / .img
MRIimage none

HOWTOs

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