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'''Diffusion <abbr title="Magnetic Resonance Imaging">MRI</abbr>'''


== Neuroscience Collaborations ==
== Neuroscience Collaborations ==
Line 7: Line 5:
{| {{Prettytable}}
{| {{Prettytable}}
|-
|-
! {{Hl2}} | Project
! {{Hl2}} rowspan="2" | Project
! {{Hl2}} | Location
! {{Hl2}} rowspan="2" | Location
! {{Hl2}} | Collaborators
! {{Hl2}} rowspan="2" | Collaborators
! {{Hl2}} | Dataset Date Received / Path
! {{Hl2}} rowspan="2" | Dataset Date Received / Path
! {{Hl2}} | Status
! {{Hl2}} colspan="8" | Status
! {{Hl2}} | Scanner
! {{Hl2}} colspan="2" | Scanner
! {{Hl2}} | Format
! {{Hl2}} rowspan="2" | Format
! {{Hl2}} | &#035; Scans
! {{Hl2}} rowspan="2" | &#035; Scans
! {{Hl2}} | Resolution (voxels)
! {{Hl2}} rowspan="2" | Resolution (voxels)
! {{Hl2}} | Voxel Size (mm)
! {{Hl2}} rowspan="2" | Voxel Size (mm)
! {{Hl2}} | Orientation
! {{Hl2}} rowspan="2" | 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 $G/data/diffusion?">F</abbr>
! {{Hl2}} | <abbr title="DWIs converted to MriImage?">M</abbr>
! {{Hl2}} | <abbr title="Tensors fit?">T</abbr>
! {{Hl2}} | <abbr title="Tubes generated?">U</abbr>
! {{Hl2}} | <abbr title="Works in Brainapp?">B</abbr>
! {{Hl2}} | <abbr title="Field strength">F</abbr>
! {{Hl2}} | <abbr title="Brand/Manufacturer">B</abbr>
|-
|-
| {{Hl2}} | Cognitive Aging
| {{Hl2}} | Cognitive Aging
Line 26: Line 35:
| content = <code>$G/data/diffusion/st_louis/cognitive_aging.2008.07.20</code>
| content = <code>$G/data/diffusion/st_louis/cognitive_aging.2008.07.20</code>
}}
}}
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 24ex; | contentcss = font-size: 90%; width: 24ex;
| {{yes}}
| header = '''Not processed'''
| {{yes}}
| content = Single dataset needs to be processed ASAP for social reasons
| {{yes}}
}}
| {{yes}}
| ??
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| {{?}}
| [[Interfile]]
| [[Interfile]]
| 1
| 1
| 83x110x64 x 36 DWIs
| 83x110x64 x 36 DWIs
| 2.0x2.0x2.0
| 2.0x2.0x2.0
| ??
| {{?}}
|-
|-
| {{Hl2}} rowspan="2" | Fibers at Risk
| {{Hl2}} rowspan="2" | Fibers at Risk
| Colorado
| Colorado
| Jack Simon
| Jack Simon
| ??
| {{?}}
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 24ex; | contentcss = font-size: 90%; width: 24ex;
| {{yes}}
| header = '''Not downloaded'''
| {{yes}}
| content = Longitudinal data and old proof-of-concept data need to be loaded into <code>$G/data/diffusion</code>
| {{no}}
}}
| {{no}}
| 1.5T ??
| {{no}}
| ??
| {{no}}
| ??
| {{no}}
| ??
| {{no}}
| ??
| 1.5T
| ??
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
|-
|-
| Portland
| Portland
| Jack Simon ([[wikipedia:VA Hospital|VA]]),<br/>Bill Rooney ([[wikipedia:OHSU|OHSU]] AIRC)
| Jack Simon ([[wikipedia:VA Hospital|VA]]),<br/>Bill Rooney ([[wikipedia:OHSU|OHSU]] AIRC)
| ??
| {{?}}
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 24ex; | contentcss = font-size: 90%; width: 24ex;
| {{no}}
| header = '''Not collected'''
| {{no}}
| content = Still waiting for the 7T protocol to finalize
| {{no}}
}}
| {{no}}
| 7T GE
| {{no}}
| ??
| {{no}}
| ??
| {{no}}
| ??
| {{no}}
| ??
| 7T
| ??
| GE
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
|-
|-
| {{Hl2}} rowspan="3" | HIV
| {{Hl2}} rowspan="3" | HIV
| Memorial Hospital
| Memorial Hospital
| rowspan="3" | Steve Correia,<br/>Ron Cohen
| rowspan="3" | Steve Correia,<br/>Ron Cohen
| ??
| {{?}}
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 24ex; | contentcss = font-size: 90%; width: 24ex;
| {{yes}}
| header = '''Not downloaded'''
| {{yes}}
| content = All the old data need to be transferred from <code>/map/gfx0/common0/diffusion/Interface/data</code>, cleaned up, and upgraded to the current pipeline
| {{yes}}
}}
| {{no}}
| 1.5T ??
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| 1.5T
| {{?}}
| [[DICOM]]
| [[DICOM]]
| ??
| {{?}}
| 256x256x90 ?
| 256x256x90 ?
| 0.8477x0.8477x1.667
| 0.8477x0.8477x1.667
| ??
| {{?}}
|-
|-
| rowspan="2" | Brown Life Sci
| rowspan="2" | Brown Life Sci
Line 86: Line 115:
| content = <code>$G/data/diffusion/brown3t/302CK.2007.11.30</code>
| content = <code>$G/data/diffusion/brown3t/302CK.2007.11.30</code>
}}
}}
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 24ex; | contentcss = font-size: 90%; width: 24ex;
| {{yes}}
| header = '''Not processed'''
| {{yes}}
| content = cad has converted to MRIimage but hasn't run the full pipeline
| {{yes}}
}}
| {{yes}}
| rowspan="2" | 3T ??
| {{yes}}
| ??
| {{no}}
| {{no}}
| {{no}}
| rowspan="2" | 3T
| rowspan="2" {{?}}
| {{?}}
| 1
| 1
| ??
| {{?}}
| ??
| {{?}}
| ??
| {{?}}
|-
|-
| {{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 101: Line 135:
| content = <code>$G/data/diffusion/brown3t/cohen_hiv_study.2008.07.21</code>
| content = <code>$G/data/diffusion/brown3t/cohen_hiv_study.2008.07.21</code>
}}
}}
| Processed
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| [[NIfTI]]
| [[NIfTI]]
| 10
| 10
| 128x128x70 x 74 DWIs
| 128x128x70 x 74 DWIs
| 1.76562x1.76562x1.8
| 1.76562x1.76562x1.8
| ??
| {{?}}
|-
|-
| {{Hl2}} | Macaques
| {{Hl2}} | Macaques
Line 115: Line 156:
| content = <code>$G/data/diffusion/caltech/macaque.2008.05.21</code>
| content = <code>$G/data/diffusion/caltech/macaque.2008.05.21</code>
}}
}}
| Processed
| {{yes}}
| ?? Bruker
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| Bruker
| [[DICOM]]?
| [[DICOM]]?
| 1
| 1
| 98x110x130 x 36 DWIs
| 98x110x130 x 36 DWIs
| 0.6x0.6x0.6
| 0.6x0.6x0.6
| ??
| {{?}}
|-
|-
| {{Hl2}} rowspan="3" | SA HIV
| {{Hl2}} rowspan="3" | SA HIV
Line 130: Line 179:
| content = <code>$G/data/diffusion/south_africa/normal.2007.10.22</code>
| content = <code>$G/data/diffusion/south_africa/normal.2007.10.22</code>
}}
}}
| Processed
| {{yes}}
| ??
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| {{?}}
| [[DICOM#Mosaic|DICOM Mosaic]]
| [[DICOM#Mosaic|DICOM Mosaic]]
| 1
| 1
| 127x128x70 x 40 DWIs
| 127x128x70 x 40 DWIs
| 1.71875x1.71875x1.7
| 1.71875x1.71875x1.7
| ??
| {{?}}
|-
|-
| {{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 142: Line 199:
| content = <code>$G/data/diffusion/south_africa/normal.2008.05.06.average1</code><br/><code>$G/data/diffusion/south_africa/normal.2008.05.06.average2</code><br/><code>$G/data/diffusion/south_africa/hiv.2008.05.09</code>
| content = <code>$G/data/diffusion/south_africa/normal.2008.05.06.average1</code><br/><code>$G/data/diffusion/south_africa/normal.2008.05.06.average2</code><br/><code>$G/data/diffusion/south_africa/hiv.2008.05.09</code>
}}
}}
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 24ex; | contentcss = font-size: 90%; width: 24ex;
| {{yes}}
| header = '''Not processed'''
| {{yes}}
| content = HIV is done but average1 and average2 seem not to have been processed yet
| {{yes}}
}}
| {{yes}}
| ??
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| {{?}}
| [[DICOM#Mosaic|DICOM Mosaic]]
| [[DICOM#Mosaic|DICOM Mosaic]]
| 3
| 3
| 127x127x75 x 66 DWIs
| 127x127x75 x 66 DWIs
| 1.71875x1.71875x1.7
| 1.71875x1.71875x1.7
| ??
| {{?}}
|-
|-
| {{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 157: Line 219:
| content = <code>$G/data/diffusion/south_africa/hiv_positive_apathy_negative_15patients.2008.07.24</code>
| content = <code>$G/data/diffusion/south_africa/hiv_positive_apathy_negative_15patients.2008.07.24</code>
}}
}}
| '''Not processed'''
| {{yes}}
| ??
| {{yes}}
| ??
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| {{?}}
| {{?}}
| 15
| 15
| ??
| {{?}}
| ??
| {{?}}
| ??
| {{?}}
|-
|-
| {{Hl2}} rowspan="2" | Tumors
| {{Hl2}} rowspan="2" | Tumors
Line 172: Line 242:
| content = <code>$G/data/diffusion/edinburgh/tumor.2007.11.06</code>
| content = <code>$G/data/diffusion/edinburgh/tumor.2007.11.06</code>
}}
}}
| '''Not processed'''
| {{yes}}
| ??
| {{yes}}
| ??
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| {{?}}
| {{?}}
| 1
| 1
| ??
| {{?}}
| ??
| {{?}}
| ??
| {{?}}
|-
|-
| {{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 184: Line 262:
| content = <code>$G/data/diffusion/edinburgh/tumor_pilot.2008.07.24</code>
| content = <code>$G/data/diffusion/edinburgh/tumor_pilot.2008.07.24</code>
}}
}}
| '''Not processed'''
| {{yes}}
| ??
| {{yes}}
| ??
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| {{?}}
| {{?}}
| 3
| 3
| ??
| {{?}}
| ??
| {{?}}
| ??
| {{?}}
|}
|}


Revision as of 20:46, 10 September 2008

Neuroscience Collaborations

Project Location Collaborators Dataset Date Received / Path Status Scanner Format # Scans Resolution (voxels) Voxel Size (mm) Orientation
C U D F M T U B F B
Cognitive Aging St. Louis Rob Paul (UMSL),
Tom Conturo (WUSTL)
2008-07-20
Y Y Y Y N N N N ? ? Interfile 1 83x110x64 x 36 DWIs 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 10 128x128x70 x 74 DWIs 1.76562x1.76562x1.8 ?
Macaques Caltech Jason Kaufman
2008-05-21
Y Y Y Y Y Y Y Y ? Bruker DICOM? 1 98x110x130 x 36 DWIs 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 x 40 DWIs 1.71875x1.71875x1.7 ?
2008.05.09
Y Y Y Y N N N N ? ? DICOM Mosaic 3 127x127x75 x 66 DWIs 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

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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