Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Re: [Freesurfer] Slow processing of large defect
by fsbuild 03 Oct '23

03 Oct '23

External Email - Use Caution   Not clear if "8G of RAM" below means 8G is assigned to the VM, or the host machine has 8G RAM total.   Assuming the VM has ~8G assigned then the host should have 16-24G RAM total. It reads like the VM is thrashing, e.g., swapping out to disk due to lack of RAM - which can cause a crash.   I would try running the VM on a host machine that can provide more RAM.  So if the VM is currently running with 8G, then try doubling it to 16G (on a host with at least 24 or 32G RAM). - R. On 10/2/23 10:31, Pål Gunnar Larsson (pall(a)ous-hf.no) wrote:         External Email - Use Caution         Hello   I am running FS 7.4.1 on Ubuntu 22.10 on Virtualbox 21.10, having 8Gb of ram.   I am running a child-MRI where I got a message about a large defect which would run slowly or crash. FS is still running after more than 10 days (70%-100% CPU use), but there are nothing written to disk for 10 days. It is working on retesselation of defect 162. Is there any reason to wait it out? Or will the results be unpredictable?   Best   Pål G. Larsson   Ikke sensitiv   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1OOHcAMGFXzhQpjoJh4qUMUwKRZnYiAD-QRVijFXCNHjhg… Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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mri_easyreg error: Killed
by Tang, Kaibo 02 Oct '23

02 Oct '23

External Email - Use Caution Hi FreeSurfer Developers, I'm attempting to register two T2 images using mri_easyreg (FreeSurfer 7.4.1). This is what my bash code looks like: #!/bin/bash for subject in ./sub-?????.nii.gz do mri_easyreg --ref ./mni152_t2_strip.nii.gz --flo $subject \ --ref_seg ./mni152_t2_strip_parc.nii.gz \ --flo_seg "${subject/.nii.gz/_parc.nii.gz}" \ --flo_reg "${subject/.nii.gz/_moved.nii.gz}" \ --fwd_field "${subject/.nii.gz/_fwd_fld.nii.gz}" \ --thread 24 subject+=" Done!" echo $subject done This is what the output looks like when I execute the bash script: 2023-10-02 11:15:58.965124: I tensorflow/core/util/port.cc:110] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`. 2023-10-02 11:15:58.988396: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: AVX2 AVX_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. 2023-10-02 11:15:59.313149: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT using 24 threads Segmentation of reference image already exists; reading from disk Segmentation of floating image already exists; reading from disk Linear registration Computing centroids and estimating affine transform Reading reference image Deforming reference image to reference space Deforming reference segmentation to reference space Normalizing intensities of reference image Reading floating image Deforming floating image to reference space Deforming floating segmentation to reference space Normalizing intensities of floating image 2023-10-02 11:16:08.118592: E tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:266] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected 2023-10-02 11:16:08.118640: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:168] retrieving CUDA diagnostic information for host: kaibo-Alienware-Aurora-R13 2023-10-02 11:16:08.118647: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:175] hostname: kaibo-Alienware-Aurora-R13 2023-10-02 11:16:08.118766: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:199] libcuda reported version is: 510.108.3 2023-10-02 11:16:08.118794: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:203] kernel reported version is: 510.108.3 2023-10-02 11:16:08.118801: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:309] kernel version seems to match DSO: 510.108.3 UserWarning: int_downsize is deprecated, use the int_resolution parameter. UserWarning: unet_half_res is deprecated, use the svf_resolution parameter. ./easyreg.sh: line 3: 1588985 Killed mri_easyreg --ref ./mni152_t2_strip.nii.gz --flo $subject --ref_seg ./mni152_t2_strip_parc.nii.gz --flo_seg "${subject/.nii.gz/_parc.nii.gz}" --flo_reg "${subject/.nii.gz/_moved.nii.gz}" --fwd_field "${subject/.nii.gz/_fwd_fld.nii.gz}" --thread 24 ./sub-00001.nii.gz Done! When I checked the folder, I saw only the parcellation results. Neither the moved floating image nor the forward field were generated. I initially thought this might be a memory problem and I set --thread 1 but I ended up getting the same result (Killed). I've searched the list and there was another error (https://secure-web.cisco.com/1oerdskR7ZTpxdkdU8iIXVp5sQdJ_BWDnyMHH3nMMFRZxQ…) similar to mine. But I don't think mine was related. Can anyone provide any insight into this? FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Platform: Ubuntu 22.04.2 LTS I am running the script on 12th Gen Intel® Core™ i9-12900KF × 24 with a 64.0 GiB memory and NVIDIA Corporation GA102 [GeForce RTX 3090]. Thanks, Kaibo

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Infant FreeSurfer request
by Aurora Orazi 02 Oct '23

02 Oct '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to download the Infant FreeSurfer pipeline. It has been 10 days since I sent the request using this account, but I have not received any news about the outcome. I am adding here the purpose of the project I intend to use the pipeline for: The idea is to utilize MRI to investigate how maternal psychopathology and use of psychopharmacological treatments during pregnancy may affect infant brain development. I'm adding here the Freesurfer version that I am using "freesufer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460. I am not sure this is the right email address for this specific problem, if it is not, then I ask if it is possible to have the right one. I hope to hear from you soon, Best regards Aurora Orazi

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Slow processing of large defect
by Pål Gunnar Larsson 02 Oct '23

02 Oct '23

External Email - Use Caution Hello I am running FS 7.4.1 on Ubuntu 22.10 on Virtualbox 21.10, having 8Gb of ram. I am running a child-MRI where I got a message about a large defect which would run slowly or crash. FS is still running after more than 10 days (70%-100% CPU use), but there are nothing written to disk for 10 days. It is working on retesselation of defect 162. Is there any reason to wait it out? Or will the results be unpredictable? Best Pål G. Larsson Ikke sensitiv

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Fwd: Postdoctoral fellowship in radiopharmaceutics: Innis at NIH
by Douglas N. Greve 28 Sep '23

28 Sep '23

External Email - Use Caution Please contact Bob with inquiries. -------- Forwarded Message -------- Subject: Postdoctoral fellowship in radiopharmaceutics: Innis at NIH Date: Thu, 28 Sep 2023 15:11:57 +0000 From: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> To: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> External Email - Use Caution This fellowship is for someone with experience in radiochemistry who seeks training in molecular imaging. The rationale underlying this combined program is that all leading PET radiochemists are also very knowledgeable about PET imaging, including pharmacology, animal imaging, and regulatory requirements for human studies. The goal of this combined program is to train future leaders in the field of PET molecular imaging. Please forward the attached advertisement to relevant and interested parties. Bob Innis ************************************ Robert B. Innis, MD, PhD Chief, Molecular Imaging Branch National Institute of Mental Health 10 Center Drive, MSC-1026 Bldg. 10, Rm. B1D43 Bethesda, MD 20892-1026 Tel: 301-594-1368 Fax: 301-480-3610 Email: robert.innis(a)nih.gov <mailto:robert.innis@nih.gov> Branch Administrative Manager: Elizabeth Alzona Tel: 301-594-1089 Email: alzonae(a)irp.nimh.nih.gov <mailto:alzonae@irp.nimh.nih.gov> http://secure-web.cisco.com/1cu2NiF_yAv_LRbeG3tSLrzRwgvhifMD6iasg9KS9KOx7k7… <http://secure-web.cisco.com/1H3yqgPC4k8FXcyKY0ko-27zDzniCxLR2ug6swsJ7KoOpcr…> ************************************

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Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg
by fsbuild 28 Sep '23

28 Sep '23

External Email - Use Caution   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/1FTmSa1QjGMsQB8Xf5Zs… 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.Conrad(a)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/1k8eRfZmZxutbzTfMi5opOvIJvAU3A9yjOgbNxek0vGGGW…) 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-GWDBJpxLeD53b5CAywKvOfsawRYQsC…   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.conrad@umm.de https://secure-web.cisco.com/1Ys12d1Q7EjaOXQJ3u43f5YMcfnSzuXxz579PUioZIBnkd…   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 <fsbuild(a)contbay.com> Datum: Mittwoch, 27. September 2023 um 00:55 An: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Cc: "Conrad, Julian" <Julian.Conrad(a)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/1k8eRfZmZxutbzTfMi5opOvIJvAU3A9yjOgbNxek0vGGGW… https://secure-web.cisco.com/1ISJip9DWoHbMeApDNRqD9f2lcyluijXFKQrQuGiqB8rzp…     On Sep 26, 2023, at 18:01, Sorby-Adams, Annabel <ASORBY-ADAMS(a)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?us… 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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Date: Tuesday, 26 September 2023 at 17:35 To: Freesurfer support list <freesurfer(a)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_5Nf3tfTFHYuzBUKgcIyghX2882Gja50…   From: freesurfer-bounces@nmr.mgh..harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Conrad, Julian <Julian.Conrad(a)medma.uni-heidelberg.de> Date: Tuesday, September 26, 2023 at 4:38 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer(a)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(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1WzT07ap5K7I2AhkWT_MIV_xAyZTUYP9UShEb3DDRK757O…

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[WARNING: ATTACHMENT UNSCANNED]Errors in recon-all for post-operative T1 images
by Jingping Xie (SBS) 27 Sep '23

27 Sep '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare the pre-operative (pre-op) and post-operative (post-op) anatomical images for a group of patients who underwent brain tumor resection. During the operation, part of the brain tissue and the skull were removed, and I would like to mark or label the removed/changed region (both cortical and subcortical) in the pre-op intact reconstructed brain. For one sample subject (tumor on the left side), I have completed the recon-all for the pre-op T1 images without any error reported. However, for the post-op images, the key volumes such as T1/brainmask/wm.mgz were generated from recon-all steps but failed in getting almost all surfaces. The related recon-all log and T1.mgz can be found in the attachment. I wonder whether (and how to) a detailed quality check or troubleshooting could solve such recon-all errors? Could I reconstruct the post-op brain when part of the structure is missing and reach my original goal? I used FreeSurfer 7.4.1 on MacOS Ventra 13.0. Thank you for your kind assistance. Best regards, Jodie ****************************************************************************************************** Jodie J. XIE, Ph.D. School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong [40 Logo_FINAL_Email template]

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Re: [Freesurfer] Running MATLAB on a MAC PRO
by fsbuild 26 Sep '23

26 Sep '23

External Email - Use Caution  You can try using the fs_install_mcr script to install the matlab runtime environment instead of using a generic or full install of Matlab on the machine.  Below the PATH to FREESRUFER_HOME is listed as /Applications/freesurfer/7.4.1, but you should change it to be whatever you installed on your machine.   The 7.4.1 release was tested with R2019b $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh <... output showing SUBJECTS_DIR and other environment variables> $ cd  $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b I think that sets things up so the libmwm* libraries are in the freesurfer tree under the path, $FREESURFER_HOME/MCRv97/bin/glnxa64.- but you should check that path. Then you can try adding the path you verified, e.g., $FREESURFER_HOME/MCRv97/bin/glnxa64,  to the head of LD_LIBRARY_PATH and remove any other entries to a different MATLAB distribution. - R.. On Sep 26, 2023, at 18:13, Alan Francis <alandarkenergy(a)gmail.com> wrote:        External Email - Use Caution        Hi All :I just bought a 2023 MAC PRO with an M2 Ultra Chip for my lab. It's running macOS Ventura. I have installed MATLAB on it but it refuses to run in a terminal or from the Applications folder.MATLAB runs perfectly fine on my other Linux machines.The MATLAB website has very little, if outdated, help.Have any of you encountered this problem?Thanks,Alan-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of NeuroscienceUniversity of Texas, School of MedicineRio Grande ValleyTexas.                                                                                                           _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg
by fsbuild 26 Sep '23

26 Sep '23

External Email - Use Caution  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/1aFiKh6YzbcJ_9V-mQth29TZB1SeCRdpmUdrLhAH6aMS… https://secure-web.cisco.com/1M-Y1AHK0ybK-HgTbS6EGioPOtjnLKD9oxxiz5O9fG-v6v… On Sep 26, 2023, at 18:01, Sorby-Adams, Annabel <ASORBY-ADAMS(a)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?us…) Check the download is OK with the md5 command in the terminal window,$ md5 tensorflow-2.4.1-py3-none-any.whlMD5 (tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4DO 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/fspython4) Uninstall the existing tensorflow package with,$ sudo $FREESURFER_HOME/python/bin/python3 -m pip uninstall tensorflow... apart from any warnings you should see the output ...Successfully uninstalled tensorflow-2.4.15) Install the package downloaded above.  This command assumes the package is in the current directory where the command is run.$ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip install ./tensorflow-2.4.1-py3-none-any.whl... apart from warnings and output about requirements (which should all be satisfied) ...... you should see tensorflow was updated ....Successfully installed tensorflow-2.4.1CHECK THE UPDATE:$ 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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>Date: Tuesday, 26 September 2023 at 17:35To: 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 Iglesiashttp://http://secure-web.cisco.com/1DgebDH1WCLKceFhMcyIutLihRRkTXmu… <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Conrad, Julian <Julian.Conrad@medma.uni-heidelberg.de>Date: Tuesday, September 26, 2023 at 4:38 PMTo: 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.shWhen I am running the pipeline, I get the following error: Illegal instructionError 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=0.00i_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_64-7.4.12) Platform: MacOS X Darwin Hope this information is sufficient and there is an easy solution.Best regards,Julian _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Running MATLAB on a MAC PRO
by Alan Francis 26 Sep '23

26 Sep '23

External Email - Use Caution Hi All : I just bought a 2023 MAC PRO with an M2 Ultra Chip for my lab. It's running macOS Ventura. I have installed MATLAB on it but it refuses to run in a terminal or from the Applications folder. MATLAB runs perfectly fine on my other Linux machines. The MATLAB website has very little, if outdated, help. Have any of you encountered this problem? Thanks, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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