Re: [Freesurfer] Issue with mri_brainvol_stats for only some participants
mri_brainvol_stats reads the following files: mri/aseg.mgz surf/lh.white surf/rh.white surf/lh.pial surf/rh.pial mri/brainmask.mgz mri/transforms/talairach.xfm $FREESURFER_HOME/ASegStatsLUT.txt Can you check if they all exist for your subjects? Any errors if you run 'mri_brainvol_stats ' at prompt? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Carly McIntyre-Wood Sent: Tuesday, January 16, 2024 4:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Issue with mri_brainvol_stats for only some participants External Email - Use Caution Hi there, I've come across a strange issue while running some new participants through Freesurfer 7.3. A portion of participants (30%) are missing their stats files, although I have visually inspected the segmentation using Freeview and they look great. I have rerun autorecon3 and it only fixes the problem for select subjects. The exact error is below: mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed \n mri_brainvol_stats 1096 \n Segmentation fault I found one instance of this in the archives where someone recommended running: recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels However, this command exits at the same point with the same error. Thanks so much, Carly ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] Issue with mri_brainvol_stats for only some participants
Can you attach recon-all.log of a failing subject? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Carly McIntyre-Wood Sent: Tuesday, January 16, 2024 4:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Issue with mri_brainvol_stats for only some participants External Email - Use Caution Hi there, I've come across a strange issue while running some new participants through Freesurfer 7.3. A portion of participants (30%) are missing their stats files, although I have visually inspected the segmentation using Freeview and they look great. I have rerun autorecon3 and it only fixes the problem for select subjects. The exact error is below: mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed \n mri_brainvol_stats 1096 \n Segmentation fault I found one instance of this in the archives where someone recommended running: recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels However, this command exits at the same point with the same error. Thanks so much, Carly ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] Issue with mri_brainvol_stats for only some participants
External Email - Use Caution Hi there, I’ve come across a strange issue while running some new participants through Freesurfer 7.3. A portion of participants (30%) are missing their stats files, although I have visually inspected the segmentation using Freeview and they look great. I have rerun autorecon3 and it only fixes the problem for select subjects. The exact error is below: mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed \n mri_brainvol_stats 1096 \n Segmentation fault I found one instance of this in the archives where someone recommended running: recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels However, this command exits at the same point with the same error. Thanks so much, Carly ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
