You can use $SUBJECTS_DIR/fsaverage/mri/aparc+aseg.mgz (already in the volume), then use mri_label2vol (with --seg flag) and $FREESURFER_HOME/average/mni152.register.dat for the registration. The problem is that the cortical labels are all very thin and won't intersect well with your ICA volume. But that is the price you pay when trying to bring surface analysis into the volume space. doug
On 02/24/2015 04:42 PM, Bruce Fischl wrote: > I see. You could do what you want by sampling the ?h.aparc.annot into > the volume (mri_surf2vol), then mapping into MNI space (mri_vol2vol). > Actually, if you do surf2vol from fsaverage I think it's already in > MNI coords, but Doug can confirm. The problem is going to be that the > mapping won't be very accurate across subjects. You would be better > off doing it all on the surface > > cheers > Bruce > > On Tue, 24 Feb 2015, Norman Benbrahim wrote: > >> No problem, >> I want to take certain regions and use them as masks in order to >> compute the joint >> histogram between a thresholded z-score map obtained from ICA (a >> resting state >> network) masked in that region, and the variance of the BOLD image. I >> already have >> scripts set up to do this in matlab, so I would only need the atlas >> in nifti format >> so I can pick out which regions to use (using the rich club paper, >> van den Heuvel et >> al. 2011), and create masks out of those. >> >> On Tue, Feb 24, 2015 at 4:22 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> wrote: >> Hi Norman >> >> perhaps you can take a step back and tell us what you want to >> use it >> for? >> We might be able to suggest a better analysis strategy >> Bruce >> On Tue, 24 Feb 2015, >> Norman Benbrahim wrote: >> >> > Hi, >> > I want to use the Desikan-Kilany atlas to run some analysis >> in some >> regions, however >> > I am very new to freesurfer. What I would like to accomplish >> is the >> following: >> > 1) Transform the atlas into MNI152 2mm space >> > 2) Convert the atlas to a binary nifti image (similarly to >> the way >> FSL's atlases are >> > stored) >> > If anyone can help me get started that would be awesome. >> Thank you! >> > -Norman >> > >> > >> _______________________________________________ >> 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. >> >> >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
