In tkmedit on fsaverage? I just ran something similar (using your /lh.amyg.faceaw.5.3CRFH.anatconstr.p05.n65.label) and it seemed to give the correct results. I viewed it with
tkmedit -f /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz -aux dougvolume.nii.gz -ov dougvolume.nii.gz -fminmax .5 1 doug On 07/26/2015 04:28 PM, Barbour, Tracy,M.D. wrote: > 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 > > -- 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.
