Dear Freesurfer Developers,
I have recently downloaded Freesurfer 7.2.0 and am trying to run the hippocampal segmentation. I tried installing the Matlab 2014b compiler but when I run the command:
sudo FREESURFER_HOME=$FREESURFER_HOME fs_install_mcr 2014b
it repeatedly gives me the error:
./install: line 334: /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.6Gemf2Ah/bin/unknown/install_unix: No such file or directory
ls: /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.6Gemf2Ah/install-target/v*: No such file or directory
Following this I am unable to run the hippocampal subfield segmentation.
Additionally, I also tried downloading the compiler separately and copying the bin/maci64 folder into a new directory under the freesurfer root directory labelled “MCRv84”. When I do this, it starts running for a second but then
gives me the following error:
Setting up environment variables
---
DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0/MCRv84//bin/maci64:/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0/lib/gcc/lib:
dyld[85643]: Library not loaded: @rpath/libmwmclmcrrt.8.4.dylib
Referenced from: /Applications/freesurfer/7.2.0/MCRv84/bin/maci64/libmwlaunchermain.dylib
Reason: tried: './libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64/libmwmclmcrrt.8.4.dylib'
(no such file), '/Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/lib/gcc/lib/libmwmclmcrrt.8.4.dylib'
(no such file), '/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84/bin/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84/bin/maci64/./libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84/bin/maci64/../../sys/os/maci64/libmwmclmcrrt.8.4.dylib'
(no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/./libmwmclmcrrt.8.4.dylib'
(no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/../../sys/os/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/libmwmclmcrrt.8.4.dylib'
(no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/./libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/../../sys/os/maci64/libmwmclmcrrt.8.4.dylib'
(no such file), '/usr/local/lib/libmwmclmcrrt.8.4.dylib' (no such file), '/usr/lib/libmwmclmcrrt.8.4.dylib' (no such file)
/Applications/freesurfer/7.2.0/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: 85643 Abort trap: 6
/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML BIOC_0001_v01_T1_FS /Users/ashwativipin/Desktop/Freesurfer/Stats/
0.333333333333333333333333333333333333 /Applications/freesurfer/7.2.0/average/HippoSF/atlas/AtlasMesh.gz /Applications/freesurfer/7.2.0/average/HippoSF/atlas/AtlasDump.mgz /Applications/freesurfer/7.2.0/average/HippoSF/atlas/compressionLookupTable.txt 0.05
left L-BFGS v21 '/Applications/freesurfer/7.2.0/bin/fs_run_from_mcr /Applications/freesurfer/7.2.0/bin/' 0
Darwin Ashwatis-MacBook-Pro.local 21.3.0 Darwin Kernel Version 21.3.0: Wed Jan 5
21:37:58 PST 2022; root:xnu-8019.80.24~20/RELEASE_ARM64_T8101 arm64
T1 hippocampal subfields exited with ERRORS at Mon Apr 4
12:11:15 +08 2022
For more details, see the log file /Users/ashwativipin/Desktop/Freesurfer/Stats//BIOC_0001_v01_T1_FS/scripts/hippocampal-subfields-T1.log
I have also attached the log file for you. Could you please help? I’m not sure what I’m doing wrong since the above steps worked just fine a few months ago. I also have matlab 2022 installed and am wondering if that could be interfering
with this?
Thanks so much! Hope to hear from you soon.
Best,
Ashwati
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