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.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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