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Thanks for reporting this. This posting indicates there is a difference in defining that for arm64 compared to intel architectures, https://secure-web.cisco.com/1FTmSa1QjGMsQB8Xf5Zs5AKj4Xk9F312HcVmOIIHIT5kDUDgCxaV4sUSYmWuRa96GF1JL06qjFzBNdpYJJmJtR_3GjMMsisKAkzdiR-9ZBMQ0UGgMFV1FMSpcTLB_xGSq00DSHrWzdrEfSjrszCjHWsweQfauiFuLs2xdeD1eT0PtzAhCwyK4YRNAxKIymf3B2xgRChAGuCAADy3dvKEuQlT1yW9e-XxoMNoOtWuuVrBeO2Q9y2k2MYY7UKxEf-GwVuJjm1SXJMEk-xcM_MzGdfRErVA1oHtLUe91iMGr3w5n81jieFowP5WqliBQChGiNpC5ROUEPBKC68P_B7aNafTnqMUUxJHq1nNq-QPVwXU/https%3A%2F%2Fwww.reddit.com%2Fr%2FUbuntu%2Fcomments%2Fpfabeq%2Fsolved_problem_float128_in_arm64%2F%3Frdt%3D45747 We will look into it along with producing an updated arm64 build. You could try making the change described in the posting in the SynthSeg code if you like. You will not encounter that error in any existing/previous release, 7.4.1 ... 7.3.2 as you are using a new arm64 development build which is post the 7.4.1 release. - R. On 9/28/23 07:20, Conrad, Julian (julian.con...@medma.uni-heidelberg.de) wrote: Hello again FreeSurfer Developers, I'm attempting to do a surface reconstruction from a GRE magnitude image using recon-all-clinical.sh As was stated before, there seem to be issues with the current Mac processors. so I downloaded the dev version (https://secure-web.cisco.com/1k8eRfZmZxutbzTfMi5opOvIJvAU3A9yjOgbNxek0vGGGW2QZ0blD-OpKmgogA7x9_rAfwfIcEGnZ7E8kgb9XNIzx2xLxQewJp32hJt31QUUAewAp1K7-Yjwk7lXCYxbaGdw8dtRE5zMFil4OqFhzHgZY7gNWOXHrgQ1zq6WrtnIl3Pllv0QaHc4JShUbdyQSVyQNgVymwLgj-PtjkDzhnise1J5RVUUczUi0PIoIHjn-dH5Ex7dw4_Tj8IUVRY1qDYHEdyBacN3YGVr6RlpLul0aH5727rGjfiCIau2iHg42KAJrBDTHZI1-iNSQ3tkbKJHbmkjy3X3wvfogE4XxSKFEkJaGyNNvit377-Ejbu0/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg) as was suggested by your team. Now it started to run. But I got this error: File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/numpy/__init__.py", line 320, in __getattr__ raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'float128' Error in SynthSeg (see also attached recon log) My numpy version is 1.26, python 3.9.6 I tried to change the float specifications using this but this did not do the job https://secure-web.cisco.com/1Nw2CoSnBRIpwTK-GWDBJpxLeD53b5CAywKvOfsawRYQsCt_nqIiIgvTq2J_n4k1ncOfN0_1YRFNw_yiQfCaYvq7eGL7mh7nrzrvKKlQPHdiBDIJjRSrLSwF2ord-O-WSRM-NviF0EKgGiF2UKK3JW3seF0e8OvmTk9PjKYSyYaHsb-tyVc_4U3HLYcI1gW3Vy3wlhNB1UswTFvC6ZytgyLo5yrnncdt-l8NY3IQCvMy0I1eEd39yhIVSSZG1AyUvSGpe1Vl4NWMJKf_finRkqZwY3bVrUdW2uJLPCUjW9uUH-9_ubVjK7HLys9i6T_IQR7zybKx3_HHH_gNPk-lMtA/https%3A%2F%2Flevelup.gitconnected.com%2Ffix-attributeerror-module-numpy-has-no-attribute-float-d7d68c5a4971 Do you have an idea how to fix this? Will this also occur if I opted for freesurfer 7.3.2? I am a little hesitant do install the older version just yet.. Best regards, Julian Mit freundlichen Grüßen Dr. med. Julian Conrad Oberarzt | senior physician Sektion Neurodegeneration | Division of Neurodegeneration Neurologische Klinik | Department of Neurology Universitätsmedizin Mannheim | University Medicine Mannheim Medizinische Fakultät Mannheim | Medical Faculty Mannheim Universität Heidelberg| Heidelberg University Theodor-Kutzer-Ufer 1 - 3 D-68167 Mannheim Tel. +49 621 383-9025 E-Mail: julian.con...@umm.de https://secure-web.cisco.com/1Ys12d1Q7EjaOXQJ3u43f5YMcfnSzuXxz579PUioZIBnkdjMmJeiYqS72gOEML4tmdshTJVb0Gai-r0nSIwt3zUOq1rPOJ6S1vQ8jnIme23u1sHITNH3Z7pJ5bdgTqzfUu9XxZIwLJjaWguptlNBj2AFXeJ1mTOxf7FvCBoU--iGnNTVgrRGx9NtMLmWjaxXd9Vq0g8OSQ9xWjpl2AU6eHRwZcDCZTYIoAGNNJaHMl0I8K_1Pf6Y60cY6ZisRzXXbAWfYZLhjuApKw3uWiibl5Tjq6L-5Vr5S5WYIq_cZF-5VuamILUkdDSFKB-H3R79vIFA606HhbzTCE-C-jJbFSgXbA5HfsQjr3uzHI8-1mNE/https%3A%2F%2Fwww.umm.de%2Fneurologische-klinik%2Fsektion-neurodegeneration%2F Universitätsklinikum Mannheim GmbH Geschäftsführer: Freddy Bergmann, Prof. Dr. med. Hans-Jürgen Hennes | Aufsichtsratsvorsitzender: Dr. Peter Kurz Handelsregister-Nr. 7331 Mannheim | Sitz und Gerichtsstand: Mannheim Medizinische Fakultät Mannheim der Universität Heidelberg Dekan: Prof. Dr. med. Sergij Goerdt ---------- Diese E-Mail enthält möglicherweise vertrauliche und/oder rechtlich geschützte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den Absender und löschen Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail ist nicht gestattet. Universitätsmedizin Mannheim universitär - modern – menschlich Von: fsbuild <fsbu...@contbay.com> Datum: Mittwoch, 27. September 2023 um 00:55 An: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Cc: "Conrad, Julian" <julian.con...@medma.uni-heidelberg.de> Betreff: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg Besides patching the python distribution, another option available now is the development arm64 build for silicon Macs with an M1, M2 processor. But this is not a release build and so has not been tested like a stable release. The dev builds are currently ~3 months post the 7.4.1 release from back in June of this. year. We’d be happy to hear how it goes if you try it. The download links are below. - R. https://secure-web.cisco.com/1k8eRfZmZxutbzTfMi5opOvIJvAU3A9yjOgbNxek0vGGGW2QZ0blD-OpKmgogA7x9_rAfwfIcEGnZ7E8kgb9XNIzx2xLxQewJp32hJt31QUUAewAp1K7-Yjwk7lXCYxbaGdw8dtRE5zMFil4OqFhzHgZY7gNWOXHrgQ1zq6WrtnIl3Pllv0QaHc4JShUbdyQSVyQNgVymwLgj-PtjkDzhnise1J5RVUUczUi0PIoIHjn-dH5Ex7dw4_Tj8IUVRY1qDYHEdyBacN3YGVr6RlpLul0aH5727rGjfiCIau2iHg42KAJrBDTHZI1-iNSQ3tkbKJHbmkjy3X3wvfogE4XxSKFEkJaGyNNvit377-Ejbu0/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg https://secure-web.cisco.com/1ISJip9DWoHbMeApDNRqD9f2lcyluijXFKQrQuGiqB8rzpImtFabgcaux9ndW9-G5RhmJNOcEQ9-gd-fykVbei9vIpDU6U6WOAGPq6mPgYiSQQoW2Px7Ob2Zo_FXId8Wx1NjQziQSpvypF0SdYASNSoHvjBlcM4teP8oQ389tlm8rAvEGeOyYjHTb9NxcM-FdqktYepdMb_AI7h0QYPhabKdLx7ov_zmUGt0DF-3KCJ-MxFWG_j5iPxQjdl_fbmnVILtM5TQEMRxhsEkVljqDwES3VUZmlJkR0Zrgekgl9LXYgMI3r8b_xbKEHB5nIhkyntGM3k1RD6bPsrH_VUDBosDDgqVZDHDBYGgsLFiI2ZY/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.tar.gz On Sep 26, 2023, at 18:01, Sorby-Adams, Annabel <asorby-ad...@mgh.harvard.edu> wrote: 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, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://drive.google.com/file/d/15Qeve5FIA137KON67ehKIOyXy1N0PbAC/view?usp=share_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/15K8tGUf8tZtMuq_5Nf3tfTFHYuzBUKgcIyghX2882Gja50a6uIEDG7cSARtXacblPJy1IZsF_YmxNJ_anGX4Z8Qb-AH9GlhFzQY_gKgZlh3uUbpSc5cQLMmlsmexPavaiWDUPUzftKvfbPBFQ8Emi67KBJIrpPDY1D_xJP_TwrQtKUWkI14bf1bysv1JeTf4r6q6H7LDOrll1Y8tuVeRW_jNnlor04QHVeugdgMkkevUQQz4NAiQiIg1_MKoS0uPtyIKM6Gi7FuTZkBDzMe6SkBF7pPhybmRtnPrSKR8uNmU5U5aF8B0vGM9ukBZkj7Fi9TeFAkNKn5EQV7FnqYSaQ/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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1WzT07ap5K7I2AhkWT_MIV_xAyZTUYP9UShEb3DDRK757O3aTYhDlk7dbJ42YjbduQj-5vXXR8KGnBOL96aJJOgRyJi2pQJVZvuvlTUFZYkyVpuyxBioVyCBdccWUjcmGYXGx0P1wkgsYHdeHSL0ZKbKNuZ4vswO7-FrJNwpMAPaAs__fB_P0_q1IgKI9IilcrGn2ZTb_1eR2w70wkVh5rw34xU2APyTeI46nZM2mQxa36MTc8A-0R6IQRI-tv73DlkRaNKuYwtcCujEopmIsW35rD6ps4mdQi7nf_GeLIOOTyTNKvbwjtXCtU_rN25lK6NA0P3oFp-tBi1UVNI2ZOg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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