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