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
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 My Google Calendar http://secure-web.cisco.com/1fTLLOHBUxeHr_93Qy3ygesltkiuCLo-hiJm1MHYChZYxiujW7jC7dSbyppZUA8TD1amrbBBoAQ94IGFiELJHYJwCQgKT26mPOEV5MnZCH_C7I2Kl1QyYUWPF_3ID6sWeQVIX6tlV3lcmEItCxtiSMUO2-CXN3krd0J1yvXH4Gga1ljAjU71eif3so2Wd0VxHMjurSKqNHE8CHj-P4cphT4P204F64moZSZplHSBbanKd9mSVgTPmrItidsCVg82fjQAlCvTla7ffJBuILq2hMpn1g_br2ns_ZqVLwj2M9_3r57yRpRhM9oXgaPme9Zjs/http%3A%2F%2Fwww.google.com%2Fcalendar%2Fembed%3Fsrc%3Djames.hengenius%40gmail.com
Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
External Email - Use Caution
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 availableVolume 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 CautionHi 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
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
https://secure-web.cisco.com/15Q0jh3Ok66VhYe8opg6hHV41Nr-_F8xJen-uLAK-BIWnzC... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1NSAgquM4SzFg6eUtY6OXZFAOWpAFgKsnak1OLc7yJLMs0z... < https://secure-web.cisco.com/1NSAgquM4SzFg6eUtY6OXZFAOWpAFgKsnak1OLc7yJLMs0z... .
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
James Hengenius