Sorry, I've lost track of what is going on here. How was lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz
created? On 7/23/15 12:08 PM, Barbour, Tracy,M.D. wrote: > 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 > > _______________________________________________ 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.
