Freesurfer experts,
I am interested in converting functional ROIs defined by the Greicius lab (
http://findlab.stanford.edu/functional_ROIs.html) into individual subject
space. Originally I had converted the fROIs from an FSL-based MNI152 to
Freesurfer-based MNI305 space. To do this I used this command (in this case
for the precuneus network fROI):
*mri_label2vol \*
*--seg Precuneus.nii.gz \*
*--reg $FREESURFER_HOME/average/mni152.register.dat \*
*--invertmtx --o Precuneus_FS.nii.gz \*
*--temp $FREESURFER_HOME/subjects/fsaverage/mri/mni305.cor.mgz*
*The output file's information, provided by 3dinfo, is as follows:*
Template Space: ORIG
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 67,108,864 (67 million [mega]) bytes
Geometry String: "MATRIX(1,0,0,-128,0,0,-1,128,0,-1,0,128):256,256,256"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Superior-to-Inferior
third (z) = Posterior-to-Anterior [-orient RSP]
R-to-L extent: -128.000 [R] -to- 127.000 [L] -step- 1.000 mm [256
voxels]
A-to-P extent: -127.000 [A] -to- 128.000 [P] -step- 1.000 mm [256
voxels]
I-to-S extent: -127.000 [I] -to- 128.000 [S] -step- 1.000 mm [256
voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is float
I would like to take the output of this command and convert it to an
individual subject's space. However, I'm not really sure how to proceed.
Originally I thought the above command, in using the mni305.cor.mgz file in
fsaverage's mri folder, would put the output file into fsaverage's space. I
could then, I figured, use some other commands I have for moving things in
fsaverage space to individual subject space. Unfortunately, when I try to
load the above output file into tkmedit for fsaverage as an aux volume it's
essentially off screen (i.e. not in the brain). Obviously the output file
is not in fsaverage space, per se.
Any thoughts on how to proceed?
Thanks,
Paul
--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
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