Dear FreeSurfer Experts,
I’m recently getting an error in make_average_subject and can’t find
the reason.
Please see the following for the error log from recon-all.log:
mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel
mri/norm.mgz mri/transforms/talairach.m3z
/home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca
mri/aseg.auto_noCCseg.label_intensities.txt
relabeling unlikely voxels interior to white matter surface:
norm: mri/norm.mgz
XFORM: mri/transforms/talairach.m3z
GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca
label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /home/lakshman/freesurfer/subjects
subject avgsubject1
outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0
Reading lh white surface
/home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white
Reading lh pial surface
/home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial
Loading lh annotations from
/home/lakshman/freesurfer/subjects/avgsubject1/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally
/home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)
Reading rh white surface
/home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white
Reading rh pial surface
/home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial
Loading rh annotations from
/home/lakshman/freesurfer/subjects/avgsubject1/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally
/home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from
/home/lakshman/freesurfer/subjects/avgsubject1/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from
/home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
mghRead(mri/norm.mgz, -1): could not open file
-------------------------
Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from
Could you please help us in resolving the issue.
Have also attached the recon-all log for reference.
Thanks & Regards,
Janani
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recon-all.log
Description: recon-all.log
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