External Email - Use Caution Hi Julian,
I have managed to run recon-all on my Apple M1 macOS Ventura using the 7.3.2 version of Freesurfer. It does not work on 7.4.2 or dev versions, however. These instructions were posted in a previous correspondence from fsbuild, but reposting here for anyone else having the same issue: You may not be able to run these commands without sudo/admin permissions on your machine. 1) Download the tensorflow-2.4.1-py3-none-any.whl from, https://secure-web.cisco.com/1klszb-du72zzOU81o6pWn28vjYMVSQcTmDSQ_1LxajxX2LGA-Qn7NWWyq4otvAYvgirpJZZwramc6xUHO2C1Sco6xEEPMLV5TsNecbtRMByuTaGB_p6LwlxMOIDDmgxpe_Ayf2p-nIhPny91tqK6kHa2L_AsKho73fNLGCNFsFm7yhjWRhHYS-3CluRtYkZWePoB-tkURZvGmhwzV4ENY_8MDUvUJTfxFZ9t-k5t-49gilwm_IcWpQZIFWuTEOga-GoVOxbvw9w8dXwhPWE-1yEQSY74iCf3nP7OntosrLk/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F15Qeve5FIA137KON67ehKIOyXy1N0PbAC%2Fview%3Fusp%3Dshare_link 2) Check the download is OK with the md5 command in the terminal window, $ md5 tensorflow-2.4.1-py3-none-any.whl MD5 (tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4 DO NOT PROCEED UNTIL YOU GET THE ABOVE OUTPUT FROM the md5 command. 3) Setup the Freesurfer 7.3.2 environment (shown here as installed via .pkg file under /Applications) and verify the path to fspython is from the 7.3.2 release, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.3.2-20220803-878457d -------- ... environment variable settings output ... $ which fspython /Applications/freesurfer/7.3.2/bin/fspython 4) Uninstall the existing tensorflow package with, $ sudo $FREESURFER_HOME/python/bin/python3 -m pip uninstall tensorflow ... apart from any warnings you should see the output ... Successfully uninstalled tensorflow-2.4.1 5) Install the package downloaded above. This command assumes the package is in the current directory where the command is run. $ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip install ./tensorflow-2.4.1-py3-none-any.whl ... apart from warnings and output about requirements (which should all be satisfied) ... ... you should see tensorflow was updated .... Successfully installed tensorflow-2.4.1 CHECK THE UPDATE: $ which fspython /Applications/freesurfer/7.3.2/bin/fspython $ fspython >>> import sys, os >>> import tensorflow >>> You should see the prompt return to ">>>" after the import of tensorflow with no errors reported. Hit Ctrl-D to escape the python session. The update should now be complete. Once you have done this you should be able to run recon-all via 7.3.2. Hope this works! Annabel From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu> Date: Tuesday, 26 September 2023 at 17:35 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg External Email - Use Caution Dear Julian, I believe this is a problem with SynthSeg not being compatible with the new microprocessor in MAC computers. Our software engineers are looking into solutions to this. Sorry for the inconvenience, Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1Gpz43kiNknL9BKam5I7Djq85LOKVEn0-BDgYtOhgMCQJHuiwj-Za5vRUdJKZdPavOCSBV_POBXbo-JtObaxDBYc2zyZNSCWXV2u1rnluFwsXFJjjFfJgCqK1QsW6LWmh0V6vzP2AO_yPaw2XQxac7f1FAhNb-5PQqDBEViNWskat2B4H596Yc40XZZrkaP3Z2u_uuDHeKYhhHQ02vg-8vvGSBtrTqv3aG9CBqgaLSZVFpOMSPbdrc_BdgFbl9YgcKsxP5OyAUcWIpmjtXCnsjw/http%3A%2F%2Fwww.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Conrad, Julian <julian.con...@medma.uni-heidelberg.de> Date: Tuesday, September 26, 2023 at 4:38 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to do a surface reconstruction from a GRE magnitude image using recon-all-clinical.sh When I am running the pipeline, I get the following error: Illegal instruction Error in SynthSeg neuroadmin@medma0236 ~ % recon-all-clinical.sh /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii RC026_sub-010_ses-mri01 8 /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer #-------------------------------------------- #@# recon-all-clinical Di 26 Sep 2023 21:53:31 CEST mri_convert /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz reading from /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii... TR=49.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.997386, 0.00125151, 0.0722456) j_ras = (2.37011e-10, 0.99985, -0.0173204) k_ras = (-0.0722564, 0.0172751, 0.997236) writing to /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz... Illegal instruction Error in SynthSeg 1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1 2) Platform: MacOS X Darwin Hope this information is sufficient and there is an easy solution. Best regards, Julian
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