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 2: Line 2:


== 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.
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]].


{| {{Prettytable}}
{| {{Prettytable}}
Line 16: Line 21:
! {{Hl2}} rowspan="2" | # DWIs
! {{Hl2}} rowspan="2" | # DWIs
! {{Hl2}} rowspan="2" | Voxel Size (mm)
! {{Hl2}} rowspan="2" | Voxel Size (mm)
! {{Hl2}} rowspan="2" | Orientation
! {{Hl2}} colspan="6" | Orientation
|-  
|-  
! {{Hl2}} | <abbr title="Scans collected by collaborator?">C</abbr>
! {{Hl2}} | <abbr title="Scans collected by collaborator?">C</abbr>
Line 28: Line 33:
! {{Hl2}} | <abbr title="Field strength">F</abbr>
! {{Hl2}} | <abbr title="Field strength">F</abbr>
! {{Hl2}} | <abbr title="Brand/Manufacturer">B</abbr>
! {{Hl2}} | <abbr title="Brand/Manufacturer">B</abbr>
! {{Hl2}} | -X
! {{Hl2}} | +X
! {{Hl2}} | -Y
! {{Hl2}} | +Y
! {{Hl2}} | -Z
! {{Hl2}} | +Z
|-
|-
| {{Hl2}} | Cognitive Aging
| {{Hl2}} | Cognitive Aging
Line 51: Line 62:
| 36
| 36
| 2.0x2.0x2.0
| 2.0x2.0x2.0
| {{?}}
| colspan="6" {{?}}
|-
|-
| {{Hl2}} rowspan="2" | Fibers at Risk
| {{Hl2}} rowspan="2" | Fibers at Risk
Line 72: Line 83:
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| colspan="6" {{?}}
|-
|-
| Portland
| Portland
Line 92: Line 103:
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| colspan="6" {{?}}
|-
|-
| {{Hl2}} rowspan="3" | HIV
| {{Hl2}} rowspan="4" | HIV
| Memorial Hospital
| Memorial Hospital
| rowspan="3" | Steve&nbsp;Correia,<br/>Ron&nbsp;Cohen
| rowspan="4" | Steve&nbsp;Correia,<br/>Ron&nbsp;Cohen
| {{?}}
| {{?}}
| {{yes}}
| {{yes}}
Line 113: Line 124:
| {{?}}
| {{?}}
| 0.8477x0.8477x1.667
| 0.8477x0.8477x1.667
| {{?}}
| colspan="6" {{?}}
|-
|-
| rowspan="2" | Brown Life Sci
| rowspan="3" | Brown Life Sci
| {{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 = 2007-11-30
| header = 2007-11-30
Line 128: Line 139:
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| rowspan="2" | 3T
| rowspan="3" | 3T
| rowspan="2" {{?}}
| rowspan="3" {{?}}
| {{?}}
| {{?}}
| 1
| 1
Line 135: Line 146:
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| colspan="6" {{?}}
|-
|-
| {{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;
Line 150: Line 161:
| {{yes}}
| {{yes}}
| [[NIfTI]]
| [[NIfTI]]
| 10
| 13
| 128x128x70
| 128x128x70
| 74
| 74
| 1.76562x1.76562x1.8
| 1.76562x1.76562x1.8
| {{?}}
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-10-09
| content = <code>$G/data/diffusion/brown3t/cohen_hiv_study_registered.2007.02.07</code>
}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{n}}
| {{n}}
| {{n}}
| {{n}}
| [[NIfTI]]
| 8
| 128x128x70
| 74
| 1.76562x1.76562x1.8
| R || L || A || P || I || S
|-
|-
| {{Hl2}} | Macaques
| {{Hl2}} | Macaques
Line 178: Line 208:
| 36
| 36
| 0.6x0.6x0.6
| 0.6x0.6x0.6
| {{?}}
| colspan="6" {{?}}
|-
|-
| {{Hl2}} rowspan="3" | SA HIV
| {{Hl2}} rowspan="3" | SA HIV
Line 202: Line 232:
| 40
| 40
| 1.71875x1.71875x1.7
| 1.71875x1.71875x1.7
| {{?}}
| colspan="6" {{?}}
|-
|-
| {{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;
Line 223: Line 253:
| 66
| 66
| 1.71875x1.71875x1.7
| 1.71875x1.71875x1.7
| {{?}}
| colspan="6" {{?}}
|-
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 85ex;
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 85ex;
Line 244: Line 274:
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| colspan="6" {{?}}
|-
|-
| {{Hl2}} rowspan="2" | Tumors
| {{Hl2}} rowspan="2" | Tumors
Line 268: Line 298:
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| colspan="6" {{?}}
|-
|-
| {{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;
Line 289: Line 319:
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| colspan="6" {{?}}
|}
|}


Revision as of 23:31, 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 "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 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

Retrieved from "http://vrl.cs.brown.edu/wiki/index.php?title=Diffusion_MRI&oldid=920"