External Email - Use Caution
Hi Bruce,
Yes, everything seems normal in the input files of mri_fill. We review it slice by slice in freeview.
Do you know what could have happened?
Best regards, Marina
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Hi Marina
have you looked at the inputs to mri_fill? Does the aseg.auto_noCCseg.mgz and the wm.mgz look ok? Bruce
On Wed, 27 May 2020, Marina Fernández wrote: External Email - Use Caution Dear Freesurfer experts, When I run "recon-all -autorecon2-wm -subjid post_006" I get the following error: ... #-------------------------------------------- #@# Fill Tue May 26 16:13:33 CEST 2020 /usr/local/freesurfer/subjects/post_006/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.03994 0.01456 0.07738 -16.87541; -0.02607 1.18971 0.24142 -16.40842; -0.06544 -0.23822 1.03825 18.09422; 0.00000 0.00000 0.00000 1.00000; reading colortable from MGH file... colortable with 14176 entries read (originally /usr/local/freesurfer/FreeSurferColorLUT.txt) voxel to talairach voxel transform 1.03994 0.01456 0.07738 -16.87541; -0.02607 1.18971 0.24142 -16.40842; -0.06544 -0.23822 1.03825 18.09422; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... mri_fill: could not find any points where lh and rh wm are nbrs No such file or directory Linux sleep2014 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May 30 11:18:27 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s post_006 exited with ERRORS at Tue May 26 16:13:41 CEST 2020 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I have seen in other questions that this error may be due to the CC and the aseg files, and it is interesting because when I load aseg.auto.mgz or aseg.auto_noCCseg.mgz files in Freeview, the following message in Freeview terminal is shown in red: "colortable with 14176 entries read (originally /usr/local/freesurfer/FreesurferColorLUT.txt)", when I think they should be 1475 entries. I'm using freesurfer v6.0. Could you help me to solve this problem? Thank you in advance! Marina.
have you also looked at the talairach transform to make sure it is reasonable? And does the aseg segment the cc properly? That is, does it label it as wm as it crosses from one hemi to the other? On Thu, 28 May 2020, Marina Fernández wrote:
External Email - Use Caution
Hi Bruce, Yes, everything seems normal in the input files of mri_fill. We review it slice by slice in freeview.
Do you know what could have happened?
Best regards, Marina
Hi Marinahave you looked at the inputs to mri_fill? Does the aseg.auto_noCCseg.mgz and the wm.mgz look ok? Bruce
On Wed, 27 May 2020, Marina Fernández wrote: External Email - Use Caution Dear Freesurfer experts, When I run "recon-all -autorecon2-wm -subjid post_006" I get the following error: ... #-------------------------------------------- #@# Fill Tue May 26 16:13:33 CEST 2020 /usr/local/freesurfer/subjects/post_006/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.03994 0.01456 0.07738 -16.87541; -0.02607 1.18971 0.24142 -16.40842; -0.06544 -0.23822 1.03825 18.09422; 0.00000 0.00000 0.00000 1.00000; reading colortable from MGH file... colortable with 14176 entries read (originally /usr/local/freesurfer/FreeSurferColorLUT.txt) voxel to talairach voxel transform 1.03994 0.01456 0.07738 -16.87541; -0.02607 1.18971 0.24142 -16.40842; -0.06544 -0.23822 1.03825 18.09422; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... mri_fill: could not find any points where lh and rh wm are nbrs No such file or directory Linux sleep2014 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May 30 11:18:27 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s post_006 exited with ERRORS at Tue May 26 16:13:41 CEST 2020 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I have seen in other questions that this error may be due to the CC and the aseg files, and it is interesting because when I load aseg.auto.mgz or aseg.auto_noCCseg.mgz files in Freeview, the following message in Freeview terminal is shown in red: "colortable with 14176 entries read (originally /usr/local/freesurfer/FreesurferColorLUT.txt)", when I think they should be 1475 entries. I'm using freesurfer v6.0. Could you help me to solve this problem? Thank you in advance! Marina.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Marina Fernández