Hi Noam,

What version of FS are you using? I have incorporated a change into dev in
January. Have you seen this note?

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-January/055460.html

Lilla

On Sat, 18 Aug 2018, Peled, Noam wrote:

>
> 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
>
> ______________________________________________________________________________________________________________________________________________________________________________________________________
> From: Peled, Noam
> Sent: Saturday, August 18, 2018 3:08:22 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mri_cvs_register using fsaverage  
>
> 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
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> >
> >
>
>