Doug, Thank you for your very helpful suggestion. Indeed, doing so made it so I could quickly take any parts (or all) of each Greicius network and put them in individual subject space.
In case this may help anyone else, the final series of commands were (in this case, for the whole anterior salience network): *mni152reg --s [subj]* mri_label2vol *--seg anterior_Salience.nii.gz \* --reg $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2mm.dat \ --invertmtx --o anterior_Salience_[subj].nii.gz \ --temp $SUBJECTS_DIR/[subj]/mri/orig.mgz Cheers, Paul On Sun, Dec 1, 2013 at 7:28 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>wrote: > > Don't go through fsaverage. Instead use mni152reg to create a registration > matrix from an individual to the 152 (stored in > $SUBJECTS_DIR/$subject/mri/transforms). Then use the command below with > this registration matrix instead of mni152.register.dat > > doug > > > > On 11/27/13 2:57 PM, Paul Beach wrote: > > 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 > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology
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