I can view the surface in freeview and when I load the volume, the surface and volume appear to be aligned.

The output of mris_info is below. I see that vox2ras is missing. I try using the volume's geometry when doing the surface conversion from vtk and follow up if I encounter further issues.

Best,

Jim H

mris_info ../iBEAT_longitudinal_format/1433/1433_V2/surf/lh.pial
SURFACE INFO ========================================
type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
num vertices: 159958
num faces : 319912
num strips : 0
surface area: 83349.7
vg.valid: 0
AvgFaceArea 0.260539
AvgVtxArea 0.521072
AvgVtxDist 0.840365
StdVtxDist 0.423213
ctr : (-20.0654, -0.014698, -5.59975)
original vertex space : surfaceRAS
vertex locs : surfaceRAS
Volume Geometry (vg)
volume geometry: info is either not contained or not valid.
Volume Geometry vox2ras: Not available
Volume Geometry vox2ras-tkr: Not available
cmd[0]: ProgramName: mris_convert ProgramArguments: mris_convert /mnt/f/James_to_iBEATCloudResults//subject-168/surf/subject-168-iBEAT-iso.lh.OuterSurf.WithPar.vtk /mnt/f/James_to_iBEATCloudResults//subject-168/surf/lh.pial ProgramVersion: 8.0.0 TimeStamp: 2025/04/12-15:35:04-GMT BuildTime: Feb 4 2025 01:02:41 BuildStamp: freesurfer-linux-ubuntu20_x86_64-8.0.0-20250204-0f2bd3a User: james Machine: DESKTOP-8RBOKC7 Platform: Linux PlatformVersion: 5.15.167.4-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 8.4.0
mris_info
creationtime 2025/06/19-16:48:55-GMT
sysname Linux
hostname DESKTOP-8RBOKC7
machine x86_64
surfacefile ../iBEAT_longitudinal_format/1433/1433_V2/surf/lh.pial
hemicode 0
talairach_flag 0
rescale 0.000000
nvertices 159958
nfaces 319912
total_area 83349.664062
group_avg_vtxarea_loaded 0
avgfacearea 0.260539
avgvtxarea 0.521072
avgvtxdist 0.840365
stdvtxdist 0.423213
vtx0xyz -11.761300 18.100700 -54.420700
num_intersecting_faces 17412

On Thu, Jun 19, 2025 at 12:31 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

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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