Message: 16
Date: Fri, 20 Mar 2020 10:47:41 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] SPM Volumes on FSAVERAGE surfaces
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <10178766-753c-672f-3621-725f033f5a16@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Try running recon-all on the mni152

On 3/18/2020 5:05 PM, Ryne Nichols wrote:
>
> ????????External Email - Use Caution
>
> All,
>
> I'm having trouble getting good surface projections of SPM results. My
> SPM results come from SPM normalization -- which should be MNI152 space.
>
> I'm confused because fsaverage says it is in MNI305 space.
>
> I've tried a few commands, but the two that confuses me the most is:
>
> mri_vol2surf --mov SPMT_001.nii --mni152reg --trgsubject fsaverage
> --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1
>
> Also the similar command:
>
> mri_vol2surf --mov SPMT_001.nii --reg
> $FREESURFER_HOME/average/mni152.register.dat --trgsubject fsaverage
> --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1
>
> both give results in a wildly different place on the brain than they
> should be -- it flips the SPMT_001.nii in the Y direction.
>
> If I do
>
> mri_vol2surf --mov SPMT_001.nii --regheader fsaverage --hemi lh --out
> lh_spm.mgh --projfrac-max 0 1 .1
>
> things are close, but nor exactly how they should be (it seems).
>
> Finally, if i use a surface that's in MNI152 space
> (cvs_avg35_inMNI152) things look the way they should, e.g.:
>
> mri_vol2surf --mov SPMT_001.nii --regheader cvs_avg35_inMNI152 --hemi
> lh --out lh_spm.mgh --projfrac-max 0 1 .1
>
> thank you for any help you may provide!
>
> -ryne
>
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