Hi all, I’m trying to install a Freesurfer 6 on my M1 chip Mac, but everything just does not work well.
Actually Freesurfer 7 works well, but some pipelines (HCP mininal, fMRIPrep, etc) are using FreeSurfer 6, that’s why I’m turning to 6.
When I run recon-all, errors:
Fri Oct 14 11:00:51 CST 2022
mri_nu_correct.mni done
\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n
talairach_avi log file is transforms/talairach_avi.log...
Started at Fri Oct 14 11:00:51 CST 2022
Ended at Fri Oct 14 11:01:22 CST 2022
talairach_avi done
\n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n
#--------------------------------------------
#@# Talairach Failure Detection Fri Oct 14 11:01:24 CST 2022
/Applications/freesurfer/subjects/seg/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6010, pval=0.2817 >= threshold=0.0050)
\n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Applications/freesurfer/subjects/seg/mri/transforms/talairach_avi.log \n
\n tal_QC_AZS /Applications/freesurfer/subjects/seg/mri/transforms/talairach_avi.log \n
ERROR: awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Applications/freesurfer/subjects/seg/mri/transforms/talairach_avi.log failed! See logfile /Applications/freesurfer/subjects/seg/mri/transforms/talairach_avi_QA.log
Darwin RunjiadeMacBook-Pro.local 21.6.0 Darwin Kernel Version 21.6.0: Wed Aug 10 14:28:23 PDT 2022; root:xnu-8020.141.5~2/RELEASE_ARM64_T6000 arm64
recon-all -s seg exited with ERRORS at Fri Oct 14 11:01:24 CST 2022
When I run freeview, it yields
2022-10-14 11:24:20.865 Freeview[66988:16153343] *** WARNING: Method userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead.
QColor::setNamedColor: Unknown color name '@Variant('
QColor::setNamedColor: Unknown color name '@Variant('
QColor::setNamedColor: Unknown color name '@Variant('
QColor::setNamedColor: Unknown color name '@Variant('
QColor::setNamedColor: Unknown color name '@Variant('
QColor::setNamedColor: Unknown color name '@Variant('
QColor::setNamedColor: Unknown color name '@Variant('
QColor::setNamedColor: Unknown color name '@Variant('
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Unknown Name on a darwin12. named RunjiadeMacBook-Pro.local by runjia Fri Oct 14 11:24:17 2022
[0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Thank you in advance!