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 <[email protected]> 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 > 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 -- [email protected] > To unsubscribe send an email to > [email protected]https://mail.nmr.mgh.harvard.edu/mailman3/lists/[email protected]/ > > > _______________________________________________ > Freesurfer mailing list -- [email protected] > To unsubscribe send an email to [email protected] > > https://secure-web.cisco.com/15Q0jh3Ok66VhYe8opg6hHV41Nr-_F8xJen-uLAK-BIWnzC69quxstvw2Ct7HR46gO4QnaKhRaVec2rB25mXQgaJWtjvziVhZf8cEr6LmxWXQlVLS3ybgaG4UZa5v_tJjTF_K10idGDQaSWcbKsGumGgw-TElH_5MlqymcSUFECAFQmwgXQecOqCTTTISFbj-TfijLqc2wfHwAqdFhuX8Ek8FSoaaThTQnVdGBaBP4G85PDaQZ9UPQOH_ZGcp5G6nHU3_Snr29lLCN-qizBSG9YZKuGqICdABk9TSY58pD8Z8Ah59OI1D8105CeLXwBcnSvMEGCk0rrHQ5umIX01xHw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F > 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/1NSAgquM4SzFg6eUtY6OXZFAOWpAFgKsnak1OLc7yJLMs0zyTWpj-v4cbIYZvA04ck6CSmuXdcCZIYF2xniPz9rx2dkq9oOb2w0YeW0VfpD0aJFg_pGU891ZgbvDKiHbGLUmyGZ7xT6U9WnrY_bPMkBA0dvPQRhIkYHaxofs4WuBv605z8Ms-A9f8TeNnjGwGhNRWd74k0uEHWMPWvwO38-3i29-9oi1zfwjKqmUt0_dkAsQi_oj48ZWclUH2u6UBpYWORnJuj7gl1webEjalS6g7QexGc1MeeO8hB2eQO0jHcqW131rNqPTpx15w3yXhHdOGjnuLBbMwHXSDRiinHw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1NSAgquM4SzFg6eUtY6OXZFAOWpAFgKsnak1OLc7yJLMs0zyTWpj-v4cbIYZvA04ck6CSmuXdcCZIYF2xniPz9rx2dkq9oOb2w0YeW0VfpD0aJFg_pGU891ZgbvDKiHbGLUmyGZ7xT6U9WnrY_bPMkBA0dvPQRhIkYHaxofs4WuBv605z8Ms-A9f8TeNnjGwGhNRWd74k0uEHWMPWvwO38-3i29-9oi1zfwjKqmUt0_dkAsQi_oj48ZWclUH2u6UBpYWORnJuj7gl1webEjalS6g7QexGc1MeeO8hB2eQO0jHcqW131rNqPTpx15w3yXhHdOGjnuLBbMwHXSDRiinHw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > -- Jim Hengenius Research Associate Paus Research Group CHU Sainte-Justine Research Centre My Google Calendar <http://secure-web.cisco.com/1XntsXv3yR9s_FAFakcvR_yC5MfHO3pnLHlZHMHf-BYof3mnlU2U5kKxnFoTude2wPf1Onyubz35LwmZQx0Md-4kbBpAPf2fLa4H5FxVttEGnIkCkpk9NYvQzrCRDyPKY4LAnUOfoEqy9QV8f1TvtgRZ5vwF1BFfJtki9QxUGdUh5z0srYVwlbYI6tsEKJtr8GKzzaEgwcBl1e8HuIJXPzf2eyq5qglOFGmEr9bcMJFqfMvURpO5rTGH7awurTBICYwRMwjMZ9MgCP9T-GeIgFFNY43Gm_c_Yi49WWCAA7F3jWjgeJhlN-48vsHDUKTmVD7FI2_J8lXlO0kYTmIsHMw/http%3A%2F%2Fwww.google.com%2Fcalendar%2Fembed%3Fsrc%3Djames.hengenius%40gmail.com>
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