I'm not sure what is going wrong here. How did you create the pvf files? Are they in the same space as your SANDI file (they should be)? You also might try using the bbr .lta file instead of the .dat file. I don't think the "No such file or directory" means  anything here (it looks like it is reading in the pvf files ok).

On 11/14/2024 1:31 PM, Lee, Hansol wrote:

Thank you for the response!

Below is the command line I used:

mri_vol2surf --srcsubject Tract_HC_001_07222016 --hemi lh --projopt /autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016/pvf --projfrac 0 --surf white --srcreg /autofs/space/rhapsody_001/users/Bay8_C1/bids/derivatives/supres/sub-001/bbr/diff_bbr_t1w.dat --src /autofs/cluster/connectome2/Bay8_C1/bids/derivatives/SANDI/supres/sub-001/sub-001-SANDI-fit_De.nii.gz --out /autofs/cluster/connectome2/Bay8_C1/bids/derivatives/SANDI/supres/surf_pvf/sub-001/lh.De.100.overlay.mgz –cortex

I have the following files pvf.gm.mgz, pvf.wm.mgz, pvf.csf.mgz, and pvf.subcort_gm.mgz in the directory: /autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016.

Please let me know if you need additional details.

Thanks!

Hansol

*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Tuesday, November 12, 2024 at 10:55 AM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] mri_vol2surf error: GM estimation couldn't find enough samples

what is your command line?

On 11/11/2024 3:47 PM, Lee, Hansol wrote:

Dear FreeSurfer developers,

I am attempting to use “mri_vol2surf” command to project output
from diffusion MRI models (e.g., DTI) onto the cortical surface.

The registration between the diffusion MRI and anatomical space
was performed using “bbregister”, and the projection works well
for different --projfrac values (e.g., 0 to 1 from the white
matter surface).

However, I encountered issues when attempting to use the
“—projopt” option to account for partial volume effects.
Specifically, I received the following errors:

“reading gm volume fraction from
/autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016/pvf.gm.mgz

reading wm volume fraction from
/autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016/pvf.wm.mgz

reading csf volume fraction from
/autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016/pvf.csf.mgz

error: No such file or directory

error: GM estimation at vno 0 couldn't find enough samples

error: No such file or directory

error: GM estimation at vno 1 couldn't find enough samples

error: No such file or directory

error: GM estimation at vno 2 couldn't find enough samples

error: No such file or directory

error: GM estimation at vno 3 couldn't find enough samples

error: No such file or directory

error: GM estimation at vno 4 couldn't find enough samples

error: No such file or directory

error: GM estimation at vno 5 couldn't find enough samples

error: No such file or directory”

In the directory, I already have “pvf.gm.mgz”, “pvf.wm.mgz”, and
“pvf.csf.mgz” files.

I searched the archive and found a similar error reported in this
thread:

_https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg72784.html_

I would greatly appreciate any insights or suggestions to resolve
this issue.

Thank you in advance for your help!

Best regards,

Hansol Lee



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