I don't know what might have happened (under the hood, mni152reg uses the FSL flirt program). If you want a non-linear registration, then you'll need to use CVS (mri_cvs_register) and choose the mni target. If you just want the aparc of the aparc+aseg, then don't go into the volume at all.
On 04/17/2018 01:57 PM, Zimmerman, Jared wrote: > > Hi All, > > I’m trying to register the aparc+aseg volumes from subject T1 space to > MNI152 space and running into problems. I’ve taken the following steps > > 1.mri152reg –s Subj241 > > 2.mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz > --mov $SUBJECTS_DIR/Subj241/mri/aparc+aseg.mgz --o > Subj241_aparc+aseg_mni2mm.nii.gz --reg > $SUBJECTS_DIR/Subj241/mri/transforms/reg.mni152.2mm.dat > > This yields an image that is rotated and shrunken relative to the > MNI152_T1_2mm template as shown in the attached image. > > I’m wondering if this is the right way to do what I’d like to do. The > reg.mni152.2mm.dat file is only a linear transform, but I’d like to > apply a non-linear transformation to the subject aparc+aseg to get it > well matched to the MNI152 template space. Some of my subjects have > atypical head shapes and I really think a non-linear warp will be > necessary to achieve a good fit. > > I’ve run the MNI152 1mm template through recon-all so I have that as a > reference. Is there a way to map volumes from one subject space to > another via fsaverage or sphere sort of like mri_label2label does for > labels? > > Alternatively, I could just calculate the appropriate T1 to MNI warps > with FNIRT or ANTs and apply those to the aparc+aseg, but I figured it > would be possible to do with FreeSurfer without calculating any new > transforms. > > Thanks, > > Jared > > > > _______________________________________________ > 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.
