Thank you Doug I tried the way you suggested and the registration actually looks worse. I also tried:
mri_label2vol --subject fsaverage --label /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage_copy/label/$label.label --o $TARGET_DIR/tracy2_$label.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --temp /autofs/cluster/maury/users/gcoombs/College_Risk/fcMRI/N12Trio_avg152T1.nii.gz Is there a step that I am missing? This is for an amygdala functional ROI that was created in tkmedit and saved as a label. Tracy ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, July 20, 2015 2:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bad registration using mri_vol2vol where did lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz come from? It must be in the space of $SUBJECTS_DIR/fsaverage/mri/orig.mgz for that transform to work On 07/17/2015 02:43 PM, Barbour, Tracy,M.D. wrote: > > > Hello, > > I'm trying to convert an ROI mask I created in MNI305 space to MNI152. > After running MRI_vol2vol the registration looks off (too anterior). > > Here are my commands: > > mri_convert -ot nii lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz > lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii > > mri_vol2vol --mov > /autofs/cluster/maury/users/gcoombs/College_Risk/fcMRI/N12Trio_avg152T1.nii.gz > --targ lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii --inv > --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat > --o new_lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii.gz > > Any ideas why the registration is off? > > Tracy > > > > _______________________________________________ > 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 _______________________________________________ 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.
