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Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline
by Mengjie Huang 14 Jun '23

14 Jun '23

External Email - Use Caution Thank you for the prompt response and looking into the issue. I just checked with the University IT, unfortunately FreeSurfer v7.4 and v7.3 requires Centos7.X + above, whereas the Artemis HPC operating system at my university is based on Centos 6.9, therefore I won’t be able to try the latest versions. Many thanks, Mengjie On 14 Jun 2023, at 2:56 am, freesurfer-request(a)nmr.mgh.harvard.edu wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1eSiMG6_a7dzke_i6VJRTX2KCsKqSrOQONW_3ygnRfMkI5… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu ---------------------------------------------------------------------- Message: 8 Date: Tue, 13 Jun 2023 16:07:34 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BL0PR04MB65315BAA0800424C60740C87FD55A(a)BL0PR04MB6531.namprd04.prod.outlook.com> Content-Type: text/plain; charset="windows-1252" External Email - Use Caution I?ll defer to our software engineering experts, but in the meantime, you could maybe try the Python version? https://secure-web.cisco.com/1Cv_49AxchVd_2vIYynJ4qP6kfmnE5Dy5Tw3AuuGeUNzzO… Cheers, /E -- Juan Eugenio Iglesias http://secure-web.cisco.com/1QfGfcEcTkVF9fEP1hlZPh1BIK3eVs0WEnf3b34X1Z7TR0_… From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mengjie Huang <mhua0773(a)uni.sydney.edu.au> Date: Tuesday, June 13, 2023 at 8:12 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline External Email - Use Caution Hello FreeSurfer developers, I am writing to seek help regarding an issue I encountered when trying to run the hippocampus subfields and amygdala nuclei segmentation pipeline (please see the error message attached below). I am running FreeSurfer V.7.1.1 on my university?s high performance computing (HPC) system. I have Matlab R2014b installed in '/usr/local/freesurfer/MCRv84?). I greatly appreciate any suggestions on how to resolve this issue. Many thanks for your time and help. ------------------------------ USER mhua0773 HOST hpc008 PROCESSID 3344 PROCESSOR x86_64 OS Linux ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Linux hpc008 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux pbsjob 6889001.pbsserver ------------------------------ freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 setenv SUBJECTS_DIR /scratch/Amy_FTD/controls_2_base/Preprocessing cd /scratch/RDS-FSC-Amy_FTD-RW/controls_2_base/Preprocessing /usr/local/freesurfer/7.1.1//bin/segmentHA_T1.sh 501_MRI1 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Tue Jun 13 13:59:28 AEST 2023 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//bin/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/freesurfer/7.1.1//lib/vtk/lib Invalid MEX-file '/tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64': /tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64: failed to map segment from shared object: Operation not permitted Error in kvlClear (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 115) MATLAB:invalidMEXFile @#@FSTIME 2023:06:13:13:59:28 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 6.47 S 0.57 U 4.19 P 73% M 201140 F 0 R 61507 W 0 c 189 w 3872 I 0 O 84184 L 18.03 17.42 13.59 @#@FSLOADPOST 2023:06:13:13:59:34 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 18.03 17.43 13.61 Linux hpc008 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Tue Jun 13 13:59:34 AEST 2023 Best regards, Mengjie -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1JMZ2dEQ4ht4om3ACrx-QJUee7pRreN3zkI_cNd0S89WYf… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1eSiMG6_a7dzke_i6VJRTX2KCsKqSrOQONW_3ygnRfMkI5… End of Freesurfer Digest, Vol 232, Issue 7 ****************************************** The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1fhh051ZnV2qe8DbvQwlEU_3QaaNGq-uAEEl4ew_4nNzoE… <https://secure-web.cisco.com/1fhh051ZnV2qe8DbvQwlEU_3QaaNGq-uAEEl4ew_4nNzoE…> . 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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Freesurfer Development Version Apple M1/2 Chip Compatability
by Sorby-Adams, Annabel 14 Jun '23

14 Jun '23

External Email - Use Caution Dear Freesurfers, A workaround was previously posted for Apple M1/2 processors to download and run the 7.3.2 release of Freesurfer (here https://secure-web.cisco.com/1rgq3XWhrkT5IzQbYknPjjI7Mi7jKtIiJWP1SE_KD5koSQ… Unfortunately, I require some tools currently available in the development version. Is there a possible workaround for Apple M1/2 chips and Freesurfer dev compatibility? Cheers! Annabel Annabel Sorby-Adams, PhD Postdoctoral Research Fellow Department of Neurology Massachusetts General Hospital Lunder 6 55 Fruit Street, Boston MA https://secure-web.cisco.com/1B91TQil3Y4INxdY8w5C3v5N-ew8l8og0Oc08GLlsPmXa-… Harvard Medical School https://secure-web.cisco.com/1yUJ5q0N36h2EgNqS9cfyhhlYpEJQJPWX8i6IfcDEPAcNs… E asorby-adams(a)mgh.harvard.edu T +1 617 251 6465 Pager ID 23944

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Error with running retinotopy glm
by Loïc Daumail 14 Jun '23

14 Jun '23

External Email - Use Caution Dear FreeSurfer experts, I am trying to perform a retinotopy analysis using fs-fast with Freesurfer version 7.3.2 on a Mac OS Monterey Version 12.6.2 Here is the error I am having (I saw this same error in the archive, but I wasn't able to find any solution email that followed regarding this issue): Saving X matrix to /Users/tong_processor/Desktop/Loic/retinotopy/old_Hojin_mri_data/F094_fsfast/sess01/bold/retinotopy.F094.07.lh/pr007/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf.Error in cond (line 35) s = svd(A);Error in fast_selxavg3b (line 389) XCond = cond(XtX);Error in sxa3 (line 9) fast_selxavg3b('/Users/tong_processor/Desktop/Loic/retinotopy/old_Hojin_mri_data/F094_fsfast/sess01/bold/retinotopy.F094.07.lh/sxa3.config.txt')Error in run (line 91) evalin('caller', strcat(script, ';')); Please see attached the code I used, and the associated files of the analysis Thanks in advance for your help! Best, -Loïc PhD candidate Vanderbilt University

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Error: MRInormFindControlPoints: could not find enough control points
by Man YANG 14 Jun '23

14 Jun '23

External Email - Use Caution Dear Freesurfer experts, I was trying this command: $ recon-all -s Desikan -i /path/to/nii -all, to generate the anno files. But it ends up with the errors of MRInormFindControlPoints: could not find enough control points The .nii file I am using is the volume of Desikan (https://secure-web.cisco.com/1oAobD21AB7j6CTjrLH5TvgaAb42Ta0SmXExD6UJ8gzF1Y…) I’m using FS v7.1.1, macOS Ventura 13.4. Any ideas how I can solve this? Enclosed please find the recon-all.log Thank you so much! Yang

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Export surface files to 3D Model including the annotation
by Falko Mecklenbrauck 14 Jun '23

14 Jun '23

External Email - Use Caution Dear freesurfer experts, I want to create 3D models (fbx or ply file) of the pial files including the annotation/coloring that is loaded. I tried to use mris_convert to make the pial file that was saved with the annotation to convert the surface into a 3D model however the mris_convert command doesn't seem to work for fbx and ply (stl works fine, but I heard stl doesn't save color information). Does anyone have experience with creating 3D models? Thanks in avance, best wishes, Falko -- Falko Mecklenbrauck, M.Sc. PhD Student University of Münster Institute of Psychology Biological Psychology Fliednerstr. 21 Room 310b Tel.: +49 251 83 34101

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[FreeSurfer] Process terminated when talairach was running
by Krystal Xiwing Yau 14 Jun '23

14 Jun '23

External Email - Use Caution Dear FreeSurfer expoerts, I am running recon-all for the subject on a HPC. It exited with error when talairach was running - it indicated "MINC_BIN_DIR: Undefined variable". The log file is attached to this email. I tried to look up the directory, which contains MINC_BIN_DIR as indicated on the <https://secure-web.cisco.com/1Yi_rx3_ryx7Z_5U9Ro-U7Ztjy451lAhdmjzkMKbcgnaOr…> forum <https://secure-web.cisco.com/1Yi_rx3_ryx7Z_5U9Ro-U7Ztjy451lAhdmjzkMKbcgnaOr…> . When I type the command, there was none: echo $MINC_BIN_DIR Any advise would be highly appreciated. Lots of thanks. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Error in longitudinal process step 3
by Taylor, Lisa 13 Jun '23

13 Jun '23

External Email - Use Caution Hi, I am trying to run the long. processing pipeline but I am having issues with step three. Here's the last lines in the recon-all log: cp -vf /dfs8/pub/ltaylor2/downs/6008/mri/transforms/6008_6008_to_6008.lta /dfs8/pub/ltaylor2/downs/6008_tp1.long.6008/mri/transforms/6008_6008_to_6008_tp1.long.6008.lta cp: cannot stat '/dfs8/pub/ltaylor2/downs/6008/mri/transforms/6008_6008_to_6008.lta': No such file or directory Linux hpc3-l18-04 4.18.0-425.10.1.el8_7.x86_64 #1 SMP Thu Jan 12 16:32:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 6008_tp1.long.6008 exited with ERRORS at Mon Jun 5 10:04:45 PDT 2023 I recognize that 6008_6008_to_6008.lta is not correct, but I am not sure why it is trying to pull a file name like this instead of the following ones that are actually in 6008_tp1.long.6008/mri/transforms/ : 6008_to_6008_tp1.lta 6008_to_6008_tp3.lta 6008_tp2_to_6008.lta bak talairach.auto.xfm talairach_avi.log talairach.lta talairach.xfm 6008_to_6008_tp2.lta 6008_tp1_to_6008.lta 6008_tp3_to_6008.lta cc_up.lta talairach.auto.xfm.lta talairach_avi_QA.log talairach.m3z talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt Here is an example of how the scripts are set up when using the HPC3. I have also attached the some output files. Let me know if any more information is needed. #!/bin/bash #SBATCH --job-name=fs_tp1_tp_long #SBATCH -A ltaylor2 #SBATCH -p free #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=1 #SBATCH --error=slurm-%J.err module load freesurfer/6.0.1 source ${FREESURFER_HOME}/SetUpFreeSurfer.sh export SUBJECTS_DIR=/pub/ltaylor2/downs #run freesurfer longitudinal workflow step 3 srun ${FREESURFER_HOME}/bin/recon-all -long 6008_tp1 6008 -all > out_fs_6008_tp1_long_output.txt Please help! Thank you, Lisa

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Error running hippocampus subfields and amygdala nuclei segmentation pipeline
by Mengjie Huang 13 Jun '23

13 Jun '23

External Email - Use Caution Hello FreeSurfer developers, I am writing to seek help regarding an issue I encountered when trying to run the hippocampus subfields and amygdala nuclei segmentation pipeline (please see the error message attached below). I am running FreeSurfer V.7.1.1 on my university’s high performance computing (HPC) system. I have Matlab R2014b installed in '/usr/local/freesurfer/MCRv84’). I greatly appreciate any suggestions on how to resolve this issue. Many thanks for your time and help. ------------------------------ USER mhua0773 HOST hpc008 PROCESSID 3344 PROCESSOR x86_64 OS Linux ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Linux hpc008 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux pbsjob 6889001.pbsserver ------------------------------ freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 setenv SUBJECTS_DIR /scratch/Amy_FTD/controls_2_base/Preprocessing cd /scratch/RDS-FSC-Amy_FTD-RW/controls_2_base/Preprocessing /usr/local/freesurfer/7.1.1//bin/segmentHA_T1.sh 501_MRI1 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Tue Jun 13 13:59:28 AEST 2023 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//bin/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/freesurfer/7.1.1//lib/vtk/lib Invalid MEX-file '/tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64': /tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64: failed to map segment from shared object: Operation not permitted Error in kvlClear (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 115) MATLAB:invalidMEXFile @#@FSTIME 2023:06:13:13:59:28 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 6.47 S 0.57 U 4.19 P 73% M 201140 F 0 R 61507 W 0 c 189 w 3872 I 0 O 84184 L 18.03 17.42 13.59 @#@FSLOADPOST 2023:06:13:13:59:34 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 18.03 17.43 13.61 Linux hpc008 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Tue Jun 13 13:59:34 AEST 2023 Best regards, Mengjie

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Postdoc position at UCL
by Holmes, Emma 13 Jun '23

13 Jun '23

External Email - Use Caution *** Please forward to any potential candidates in your networks who may be interested in this position *** I am currently advertising a postdoc position (3+ years) to join my lab, the Cognitive Hearing Lab, at UCL (London, UK). My lab combines behavioural techniques (e.g., auditory psychophysics), cognitive neuroscience (e.g., EEG, MEG, and fMRI), and computational modelling. The position is part of a Wellcome-funded grant to examine how central cognitive pathways interact with hearing loss. The appointed candidate will examine how central cognitive pathways interact with hearing loss, leading work using 7-Tesla MRI, which will allow us to estimate laminar-specific cortical responses in humans. The preferred start date for the position is September 2023. Full details and application portal: https://secure-web.cisco.com/1CvZUIQqm9iYIqFP3pabfMtqLyfiLMhvjiAgC7-1rPtBwU… Application deadline: 23rd June 2023 Feel free to get in touch with me (emma.holmes(a)ucl.ac.uk) for informal queries about the position Best wishes, Emma Emma Holmes Lecturer in Speech and Hearing Science, UCL (she/her) e-mail: emma.holmes(a)ucl.ac.uk<mailto:emma.holmes@ucl.ac.uk> website: https://secure-web.cisco.com/1uJCHQtdVZS6xFSMnVNfhv6i6G_j-KbPVmAEUsGmvnIkDZ… twitter: @Emma_Holmes_90<https://secure-web.cisco.com/1opyNiMvDGZSFHuRH2z2WASck84ATpT3APNaQ8UDftmWaJ…> Mailing Address: Department of Speech Hearing and Phonetic Sciences Chandler House 2 Wakefield Street London WC1N 1PF United Kingdom Let me know if I can make any adjustments related to disability or neurodivergence to improve how we interact. Please note that I don't expect you to respond to emails outside of your normal working hours.

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Requesting passcode for freesurfer virtual machine
by MIYASAKA Minori 12 Jun '23

12 Jun '23

External Email - Use Caution Dear Free Surfer experts, I would like you to send the passcode to use this file: “FS_7_2_0_ubuntu_18_04_06.ova.7z. Regards. Minori Miyasaka =========================================== Name:宮坂実祈 Mail:u650561g@ecs.osaka-u.ac.jp ===========================================

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