What space is the RS data in? If native functional space, I would register to the anatomical (bbregister), then use mri_vol2vol with the --fstal option
On 05/08/2014 04:31 PM, Paul Beach wrote: >> Hi Freesurfers, >> >> I have several processed resting time series files (processed through >> AFNI) and I'd like to convert them to MNI space. I have done this >> successfully for T1Volumes and some ROI masks using mri_convert and >> tried to use the same code for the resting series. However, I've run >> into a few issues - namely that the transformation cuts off part of >> the top of the cortex. >> >> My code: >> >> /mri_convert -it nii -ot mgz CleanData_RestState.nii.gz >> CleanData_RestState.mgz/ >> / >> / >> /mri_convert CleanData_RestState.mgz --apply_transform >> transforms/talairach.xfm \/ >> /-oc 0 0 0 CleanData_RestState_talairach.mgz / >> / >> / >> /mri_convert CleanData_RestState_talairach.mgz \ >> cleanData_RestState_talairach.nii.gz/ >> >> >> The final time series file, overlayed on the transformed T1Volume, is >> below. >> >> Inline image 1 >> >> Any suggestions? >> >> >> Thanks! >> -- >> Paul Beach >> DO/PhD candidate - Year VI >> Michigan State University >> - College of Osteopathic Medicine >> - Neuroscience Program >> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) > > > _______________________________________________ > 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 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.
