Diffusion MRI: Difference between revisions

From VrlWiki
Jump to navigation Jump to search
← Older editNewer edit →
Jadrian Miles (talk | contribs)
1,787 edits
Jadrian Miles (talk | contribs)
1,787 edits
Line 1: Line 1:
== Neuroscience Collaborations ==
== 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.
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 "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.
Line 26: Line 28:
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = <DATE_RECEIVED>
| header = <DATE_RECEIVED>
| content = <code><PATH_TO_DATA></code>
| content = <code><PATH_TO_DATA></code><NOTES_IF_ANY>
}}
}}
| <COLLECTED_BY_COLLABORATOR?>
| <COLLECTED_BY_COLLABORATOR?>
Line 55: Line 57:
! {{Hl2}} rowspan="2" | Location
! {{Hl2}} rowspan="2" | Location
! {{Hl2}} rowspan="2" | Collaborators
! {{Hl2}} rowspan="2" | Collaborators
! {{Hl2}} rowspan="2" | Dataset Date Received / Path
! {{Hl2}} rowspan="2" | Dataset Date Received
! {{Hl2}} colspan="8" | Status
! {{Hl2}} colspan="8" | Status
! {{Hl2}} colspan="2" | Scanner
! {{Hl2}} colspan="2" | Scanner
Line 109: Line 111:
| Colorado
| Colorado
| Jack Simon
| 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}}
| {{yes}}
| {{yes}}

Revision as of 00:11, 8 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.

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 ? ? 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

Retrieved from "http://vrl.cs.brown.edu/wiki/index.php?title=Diffusion_MRI&oldid=929"