Thanks, Andrew! On Tue, Feb 20, 2018 at 11:42 AM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote:
> Hi Scott, > > It looks like the mri_aparc2aseg binary in that patch directory was > compiled for centos. The version at the following link was compiled on OS > X: https://surfer.nmr.mgh.harvard.edu/pub/dist/ > freesurfer/dev_binaries/OSX-ElCapitan/mri_aparc2aseg > > If you download this new mri_aparc2aseg into your $FREESURFER_HOME/bin, > it should fix the issue. > > best > Andrew > > > On February 20, 2018 at 11:22:20 AM, Pruett, Scott ( > brandon_pru...@brown.edu) wrote: > > 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/subj >> ects/avgsubject1/label/lh.aparc.annot >> reading colortable from annotation file... >> colortable with 36 entries read (originally /home/lakshman/freesurfer/subj >> ects/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/subj >> ects/avgsubject1/label/rh.aparc.annot >> reading colortable from annotation file... >> colortable with 36 entries read (originally /home/lakshman/freesurfer/subj >> ects/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/subj >> ects/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/subj >> ects/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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Before >> opening any email and/or attachments, please check them for viruses and >> other defects. >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> -------------------------------------- ______________________________ >> _________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > -- > Scott Pruett, M.D., Ph.D. > General Psychiatry and R25 Research Track Resident, PGY4 > Department of Psychiatry and Human Behavior > Warren Alpert Medical School of Brown University > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Scott Pruett, M.D., Ph.D. General Psychiatry and R25 Research Track Resident, PGY4 Department of Psychiatry and Human Behavior Warren Alpert Medical School of Brown University
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