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
>
>
>
>