Another strange thing, one of the points (voxels) I'm trying to morph is 149 137 108. In Freeview, this coordinate is in the left hippocampus. When applying the morphing to our template brain, this is the terminal output: computing image for point 149 137 108 = 141.143 151.458 11.3095 But (141 151 11) is outside the template's brain.

For the registration, I'm using the following command: mri_cvs_register --mov MG122 --template colin27 --outdir /home/cashlab/mmvt_root/subjects/MG122/mri_cvs_register_to_colin27 --nocleanup --openmp 8

For applying it on the electrodes: mri_cvs_register --mov MG122 --template colin27 --outdir /local_mount/space/thibault/1/users/npeled/subjects/MG122/mri_cvs_register_to_colin27 --nocleanup --openmp 8

And for applying it on the electrodes file: applyMorph --template /autofs/space/thibault_001/users/npeled/subjects/colin27/mri/orig.mgz --transform /autofs/space/thibault_001/users/npeled/subjects/MG122/mri_cvs_register_to_colin27/combined_tocolin27_elreg_afteraseg-norm.tm3d point_list /autofs/space/thibault_001/users/npeled/subjects/MG122/electrodes/electrodes_to_morph.txt /autofs/space/thibault_001/users/npeled/mmvt/MG122/electrodes/electrodes_morph_to_colin27.txt a

Am I missing something? Thanks, Noam ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Peled, Noam NPELED@mgh.harvard.edu Sent: Thursday, February 7, 2019 10:36 AM To: Lilla Zollei; Freesurfer support list Subject: Re: [Freesurfer] applyMorph gives (10000 10000 10000) coordinates

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

Sure! Do you want the T1, or also the mri_cvs_register outputs? btw, I'm in the martinos, so you can access all my files (I wrote the full path)

Many thanks, Noam

p.s I'm using two different computers, one of them isn't in the center, and the freesurfer's version is freesurfer-linux-centos6_x86_64-dev-20180622-7758bad (hmmm, should I be worried it ends with 'bad'?) Can it cause these kinds of problems?

________________________________ From: Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Thursday, February 7, 2019 2:04 PM To: Peled, Noam Cc: Freesurfer support list Subject: Re: [Freesurfer] applyMorph gives (10000 10000 10000) coordinates

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