Hey Andrew, I am running FreeSurfer 6.0 on MacOS X and ran into the exact same issue as Janani, so I installed this patch. However, now I am getting the following error:
#@# AParc-to-ASeg aparc Tue Feb 20 11:04:08 EST 2018 /Users/scottpruett/Desktop/CSMRI/Freesurfer/601_10y_av \n mri_aparc2aseg --s 601_10y_av --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --no-relabel \n /Applications/freesurfer/bin/mri_aparc2aseg: Exec format error. Binary file not executable. Darwin scott-pruetts-computer.local 17.3.0 Darwin Kernel Version 17.3.0: Thu Nov 9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64 x86_64 recon-all -s 601_10y_av exited with ERRORS at Tue Feb 20 11:04:10 EST 2018 I've attached the recon-all.log file. Any help would be greatly appreciated. Best, Scott On Tue, Feb 20, 2018 at 10:25 AM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote: > 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 (janan...@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 > > ::DISCLAIMER:: > ------------------------------------------------------------ > ------------------------------------------------------------ > ------------------------------------------------------------ > ------------------------------------------------------------ > -------------------------------------- > The contents of this e-mail and any attachment(s) are confidential and > intended for the named recipient(s) only. 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recon-all.log
Description: Binary data
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