Hi David and Noam,

I have fixed a bug in applyMorph. If you have access to the dev version of the code base that should be available to you in a day. If not, send and email to the list and we can provide you with it. Here are the steps:

(1) Run mri_cvs_register command. As the applyMorph code currently only works with tm3d files (not m3z) you will need to use the --nocleanup flag to obtain those files.

(2) Identify your coordinates in data coordinate space. This means that you need to find the numbers on Freeview that are next to "orig X []" in the braces.

(3) Run the below command: applyMorph --template template/mri/orig.mgz \ --transform subj/cvs/combined_tocolin27_elreg_afteraseg-norm.tm3d \ point_list in_coords.txt out_coords.txt a

(4) The resulting coordinates will also be in data coordinate space in the template space.

Best, Lilla

On Fri, 15 Dec 2017, Peled, Noam wrote:

Hey David,

Have you managed to find a solution for that?

Best,

Noam

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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zhou, David Wei DWZHOU@PARTNERS.ORG Sent: Thursday, April 7, 2016 3:10:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Nonlinear CVS registration into average brain for coordinates   Hi all,

I have a data set of 14 subjects with intracranial (both cortical and subcortical) electrode implants, already recon'ed in Freesurfer, with an average brain + surface computed of these subjects. I would like to map each subject's electrode coordinates (a set of RAS points) into the average brain using a nonlinear transformation to account for individual deviations in surface topology.

I'm trying to figure out the steps that must be taken to achieve this. With my average brain as a template, it seems like I would use mri_cvs_register to produce each subject warped onto the template. After generating those warps, how does one apply the same warp to a set of coordinates, for example to find out where my electrodes end up in the template brain? Which output file in .../cvs contains the data necessary to compute the coordinates in the template?

I'd appreciate any instruction, thanks!

David