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
_________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Zhou, David Wei <dwz...@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
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