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.

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 $G/data/diffusion/st_louis/cognitive_aging.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 $G/data/diffusion/brown3t/302CK.2007.11.30	Y	Y	Y	Y	Y	N	N	N	3T	?	?	1	?	?	?	?
			2008-07-21 $G/data/diffusion/brown3t/cohen_hiv_study.2007.02.07	Y	Y	Y	Y	Y	Y	Y	Y			NIfTI	13	128x128x70	74	1.76562x1.76562x1.8	?
			2008-10-09 $G/data/diffusion/brown3t/cohen_hiv_study_registered.2007.02.07	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 $G/data/diffusion/caltech/macaque.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 $G/data/diffusion/south_africa/normal.2007.10.22	Y	Y	Y	Y	Y	Y	Y	Y	?	?	DICOM Mosaic	1	127x128x70	40	1.71875x1.71875x1.7	?
			2008.05.09 $G/data/diffusion/south_africa/normal.2008.05.06.average1 $G/data/diffusion/south_africa/normal.2008.05.06.average2 $G/data/diffusion/south_africa/hiv.2008.05.09	Y	Y	Y	Y	N	N	N	N	?	?	DICOM Mosaic	3	127x127x75	66	1.71875x1.71875x1.7	?
			2008.07.24 $G/data/diffusion/south_africa/hiv_positive_apathy_negative_15patients.2008.07.24	Y	Y	Y	Y	N	N	N	N	?	?	?	15	?	?	?	?
Tumors	Edinburgh	Mark Bastin	2007-11-06 $G/data/diffusion/edinburgh/tumor.2007.11.06	Y	Y	Y	Y	N	N	N	N	?	?	?	1	?	?	?	?
			2008-07-24 $G/data/diffusion/edinburgh/tumor_pilot.2008.07.24	Y	Y	Y	Y	N	N	N	N	?	?	?	3	?	?	?	?

Software

• Brainapp
• Diffusion Processing Pipeline
• $G/bin/mriatlas

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

• Diagnose tensor orientation problems