Hi Noam, Would it be possible fo ryou to upload a sample data set to our filesharing site? https://gate.nmr.mgh.harvard.edu/filedrop2/ Lilla
On Thu, 7 Feb 2019, Peled, Noam wrote:
Hey Lila, Sorry for the confusion, the attached file is the terminal output. Please find also the applyMorph output file.
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: Thursday, February 7, 2019 10:31 AM To: Freesurfer support list Subject: Re: [Freesurfer] applyMorph gives (10000 10000 10000) coordinates
Hi Noam,
Maybe a I am a bit confused but in the attached file I do not see the (10000 10000 10000) coordinate that correspond to invalid coordinate locations. Is the file that you attached your electrodes_morph_to_colin27.txt or is it the terminal output?
Lilla
On Thu, 7 Feb 2019, Peled, Noam wrote:
Hey all, I'm trying to morph patients' invasive electrodes into a template brain. I'm not sure why, but sometimes, the applyMorph gives me the (10000 10000 10000) coordinates for a subset of the electrodes, where the rest are ok. In the output, for those electrodes I can see it writes "not valid", but still gives reasonable coordinates and not (10000 10000 10000) For example:
applyMorph --template /autofs/space/thibault_001/users/npeled/subjects/colin27/mri/orig.mgz --transform /autofs/space/thibault_001/users/npeled/subjects/MG106/mri_cvs_register_to_colin27/combined_tocolin27_elreg_afteraseg-norm.tm3d point_list /autofs/space/thibault_001/users/npeled/subjects/MG106/electrodes/electrodes_to_morph.txt /autofs/space/thibault_001/users/npeled/mmvt/MG106/electrodes/electrodes_morph_to_colin27.txt a
Where in the output file you can see the (10000 10000 10000) coordinates. I attached the applyMorph output. btw, I'm using the Freesurfer dev version
Thanks, Noam
LZ