My guess is that the surface file is not formatted properly and/or does not have the proper geometry in it. Can you successfully run mris_info on it and load it into freeview (freeview -f surface)? When you convert to freesurfer format, try specifying the mgz file as the argument to the --geom flag to pass the geometry into it.

On 6/16/2025 11:44 AM, James Hengenius wrote:

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Hi FS list,

I have some infant native space cortical surfaces generated by another software package. I would like to 'paint' them with some volumetric ROIs also in the native space.

I noticed that mri_vol2surf has the "--vol2surf" option, which does not require typical FS output directory structure.

I first converted the vtk surfaces from the other software to FS format. Here, the left hemi surface is called lh.pial and the corresponding volume is subject-168-T1w-iso.mgz (also used as regheader volume). I'm trying abs distance projection with 5mm distance, no projmap (0 as dummy var), and nearest neighbor interp.

I get the errors below. My first guess is that using the native volume as the 'reg' argument is the issue, but any feedback is welcome!

Searched a bit, but the "could not allocate xforms" error only comes up in one other thread on the listserv, and it's about mri_convert, not mri_vol2surf.

Thanks,
Jim H.

mri_vol2surf --vol2surf \
/mnt/f/iBEAT_longitudinal_format/1433/1433_V2/subject-168-T1w-iso.mgz \
 /mnt/f/iBEAT_longitudinal_format/1433/1433_V2/surf/lh.pial  \ 
0 \ 
5 \ 
0  \ 
/mnt/f/iBEAT_longitudinal_format/1433/1433_V2/subject-168-T1w-iso.mgz \ 
novsm \ 
0 \ 
/mnt/f/iBEAT_longitudinal_format/1433/1433_V2/surf/lh.surf_ROIs

error: Cannot allocate memory
error: LTAalloc(1085915240): could not allocate xforms

--
Jim Hengenius
Research Associate
Paus Research Group
CHU Sainte-Justine Research Centre
My Google Calendar


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