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:
External Email - Use Caution
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
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