Hi Janani,
We have a patch for this bug here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
The second part of the readme file in that directory provides instructions for resolving this.
best Andrew
On February 19, 2018 at 9:40:22 AM, M Janani (jananimj@hcl.commailto:jananimj@hcl.com) wrote:
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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