Hi again,
Two things:
1. Again, what the output of "ls /Applications/freesurfer/7.2.0/MCRv84/“? 2. Copying the Matlab directory is a bad idea; just symlink it instead. Something like: sudo rm -rf /Applications/freesurfer/7.2.0/MCRv84 sudo ln -s [your_matlab_2014b_dir] /Applications/freesurfer/7.2.0/MCRv84
Cheers
Juan Eugenio Iglesias http://www.jeiglesias.com
On 4 Apr 2022, at 21:57, Ashwati Vipin (Dr) <ashwati.vipin@ntu.edu.sgmailto:ashwati.vipin@ntu.edu.sg> wrote:
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Dear Eugenio,
Unfortunately after I copy out the entire compiler contents (which has the components you listed) into /Applications/freesurfer/7.2.0/MCRv84/ , I get the following error when I try to run a subject:
<image003.png>
So I tried the fs_install_mcr 2014b again and it gave me the same set of error as yesterday. I’m not sure what I’m doing wrong. I have in the meantime also installed Matlab 2014b and copied out the “bin” folder from within Matlab 2014b but that doesn’t work either. Please help. Thank you
Best, Ashwati
-- Ashwati Vipin (PhD) Research Fellow - Dementia Research Centre Lee Kong Chian School of Medicine Nanyang Technological University, Singapore <image002.png>
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ashwati Vipin (Dr) <ashwati.vipin@ntu.edu.sgmailto:ashwati.vipin@ntu.edu.sg> Date: Monday, 4 April 2022 at 10:16 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] MCRv84 issue on Freesurfer 7.2.0 on MacOS Monterey 12.2
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Dear Eugenio,
Thanks so much for your email! Oops sorry, it looked different from the last time I asked questions on the forum haha!
I think I may be running into the issue because I only copied the “bin” folder under the /Applications/freesurfer/7.2.0/MCRv84/. I’ll copy the entire contents of the compiler and see if it runs properly and update you. Thanks so much again 😊
Best, Ashwati
-- Ashwati Vipin (PhD) Research Fellow - Dementia Research Centre Lee Kong Chian School of Medicine Nanyang Technological University, Singapore <image001.png>
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@MGH.HARVARD.EDUmailto:JIGLESIASGONZALEZ@MGH.HARVARD.EDU> Date: Monday, 4 April 2022 at 8:50 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] MCRv84 issue on Freesurfer 7.2.0 on MacOS Monterey 12.2 Dear Ashwati,
What are the current contents of /Applications/freesurfer/7.2.0/MCRv84/? It should be something like this:
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
Cheers,
/E
Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1TARGyKcpvCypKgDUofLvYZ5IAcWvRMPkOF-BwRiMb7JfiEz33urGjIGpBendCsFFQD8LWLxFPigwADAdN5x-8a5rwNVe2jPPdXgUI2oYLaP1_C6YH2FYm8xtWEenWmaT6qvx1Xk5rzQJSjmLaf6j2OwPWc5pG6c9U56twy6OG3ToBpYhhRXCTmr5pS0Op-nRLvuG9_xwpIWdxtQa3PoP6v1Mu5992nEf1FyXr7iYPl79Yb0cV7tDr26S5BizKNYzo8fIyQGEJzMqI3fOl5srxzHQ9htlvhTEy4MaJIsptMoa_IFFWCyaUeD0w7QNeIwl/http%3A%2F%2Fwww.jeiglesias.com
On Apr 4, 2022, at 00:19, Ashwati Vipin (Dr) <ashwati.vipin@ntu.edu.sgmailto:ashwati.vipin@ntu.edu.sg> wrote:
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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.
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