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.
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