Best,

Ashwati

-- 

Ashwati Vipin (PhD)

Research Fellow - Dementia Research Centre

Lee Kong Chian School of Medicine

Nanyang Technological University, Singapore

MCR_license.txt bin extern java polyspace runtime sys

VersionInfo.xml derived help mcr remote settings toolbox

appdata etc interprocess patents.txt resources src trademarks.txt

On Apr 4, 2022, at 00:19, Ashwati Vipin (Dr) <ashwati.vipin@ntu.edu.sg> wrote:

 

        External Email - Use Caution        

 

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

---

CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. 
Towards a sustainable earth: Print only when necessary. Thank you. 

<hippocampal-subfields-T1.log>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer