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Thanks Doug,
Yeah, I’m confused as to what happened with that registration too.
I just used ANTs to do the warping and that worked well. Good to know about
mri_cvs_register though, I will try to use that next time.
-jared
On 4/19/18, 12:12 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N. Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgr...@mgh.harvard.edu> wrote:
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
>
>
>
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