I made the label in tkmedit, then i used label2v Sent from my iPhone
> On Jul 24, 2015, at 12:22 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > 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 _______________________________________________ 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.
