Diffusion MRI
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.
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 | 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 | 2008-08-28
|
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 | ? | DICOM | 1 | 256x256x180 | 74 | .8828x.8828x.7 | ? | |||||||
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 | Analyze | 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 | ? | ? | NIfTI | 15 | ? | ? | ? | ? | ||||||||
| Tumors | Edinburgh | Mark Bastin | 2007-11-06
|
Y | Y | Y | Y | N | N | N | N | ? | 9 | Analyze | 1 | ? | ? | ? | ? | |||||
2008-07-24
|
Y | Y | Y | Y | N | N | N | N | ? | ? | DICOM | 3 | ? | ? | ? | ? | ||||||||
Software
- 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.
$G/bin/mriatlas— 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)
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 |