It doesn't seem to work

Here are the commands I was using:

mri_cvs_register --mov $SUBJECT --mni --outdir $SUBJECTS_DIR/$SUBJECT/mri_cvs_register_to_mni --nocleanup

applyMorph --template $SUBJECTS_DIR/cvs_avg35_inMNI152/mri/orig.mgz

--transform $SUBJECTS_DIR/$SUBJECT/mri_cvs_register_to_mni/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d

point_list $SUBJECTS_DIR/$SUBJECT/electrodes/electrodes_to_morph.txt $SUBJECTS_DIR/$SUBJECT/electrodes/electrodes_morph_to_MNI152.txt a

The file electrodes_to_morph.txt contains the electrodes in the $SUBJECT's orig space (T1 voxels)

As a sanity check, I checked the electrodes' values in brainmask.mgz. When checking the electrodes in electrodes_to_morph.txt against $SUBJECT/mri/brainmask.mgz, only a few were outside the brain. But when checking the electrodes after the morphing in electrodes_morph_to_MNI152.txt against cvs_avg35_inMNI152/mri/brainmask.mgz, at least half of them were outside the brain.

Any ideas?

Thanks,

Noam

Thanks Lilla!

A follow-up question: How can I use the applyMorph function to morph the points to the MNI152 space?

I'm trying to use the combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d file I've got from the mri_cvs_register call.

Which template should I use? I can't use fsaverage because it's in the MNI305 space. Should I use cvs_avg35_inMNI152 instead?

And to morph it to MNI305, should I use the inverse matrix of

M = [[0.9975, - 0.0073, 0.0176, -0.0429],
     [0.0146, 1.0009, -0.0024, 1.5496],
     [-0.0130, -0.0093, 0.9971, 1.1840],
     [0, 0, 0, 1.0000]]

As mentioned in the last section in http://freesurfer.net/fswiki/CoordinateSystems?

Thanks!

Noam

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lilla Zollei <lzollei@nmr.mgh.harvard.edu>
Sent: Wednesday, August 1, 2018 2:33:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_cvs_register using fsaverage

Yes, you can remove the template flag.

And no, not at the moment.

> Thanks Lilla!
>
> Just to be sure, when using the --mni flag, should I remove the --template flag?
>
> Also, is there any way I can calculate the registration directly to MNI305 and not MNI152?
>
>
> Thanks again,
>
> Noam
>
> ______________________________________________________________________________________________________________________________________________________________________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lilla Zollei <lzollei@nmr.mgh.harvard.edu>
> Sent: Wednesday, August 1, 2018 8:35:49 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mri_cvs_register using fsaverage
>
> Hi Noam,
>
> Can you can use the --mni flag?
>
> "Use the CVS atlas in MNI152 space as a target for registration (as
> opposed to the default CVS template)"
>
> Lilla
>
> On Wed, 1 Aug 2018, Peled, Noam wrote:
>
> >
> > I need to transfer one of our patient's electrodes locations (depth electrodes, they aren't located on the cortical surface) to MNI305 space.
> > For that, I'm trying to use mri_cvs_register to register the patient to fsaverage. I'm using to the following command:
> >
> >
> > mri_cvs_register --mov subjid --template fsaverage --outdir output_name --nocleanup
> >
> > And I'm getting the following error:
> > fsaverage : at least one mean and/or Gaussian curvature file is missing (.H, .K)
> >
> > Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files.
> > Any ideas?
> >
> > Thanks,
> > Noam
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
>