Freesurfer June 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
107 discussions

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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No flt available for tract training files
by Stylianos Charalampous 12 Jun '23

12 Jun '23

External Email - Use Caution Hello, I am trying to to run trac-all and I am getting the following error when using the FSL Flirt registration in the prior fitting step, due to the flt files not being available for the tract training subjects: WARN: Could not open /path/trctrain/hcp/mgh_1001/syn/acomm.flt.prep.trk for reading WARN: Error was: Can not open file WARN: Skipping to next subject Note: The reason I am using Flirt is because BBRegister requires the lh.white and rh.white files which I don't have available as I have used third party software for the brain parcellation. I have also had an issue with the fs_temp_file function which gives an error in cases where the subject is given as a nested folder, e.g. subject_1/subject_1_visit_1, subject_1/subject_1_visit_2 instead of subject_1_visit_1, subject_1_visit_2. This error was only noticed in the prior fitting step where the ntest was appended before subjid thus creating a file /tmp/1.subject_1/subject_1_visit_1.txt for instance causing an error. -- Kind regards, Stylianos Charalampous

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Re: [Freesurfer] Longitudinal SAMSEG with multi-contrast data
by Cerri, Stefano,PHD 12 Jun '23

12 Jun '23

External Email - Use Caution Hi Gonzalo, Assuming that you have run mri_robust_template and obtained longitudinally registered images (e.g., tp0_t1_reg.mgz, tp1_t1_reg.mgz, etc...), then you can co-register each additional contrast of each time point with the commands: mri_coreg --mov tp0_flair.nii --ref tp0_t1_reg.mgz --reg tp0_FLAIRtoT1.lta mri_vol2vol --mov tp0_flair.nii --reg tp0_FLAIRtoT1.lta --o tp0_flair_reg.mgz --targ tp0_t1_reg.mgz for time-point 0 and mri_coreg --mov tp1_flair.nii --ref tp1_t1_reg.mgz --reg tp1_FLAIRtoT1.lta mri_vol2vol --mov tp1_flair.nii --reg tp1_FLAIRtoT1.lta --o tp1_flair_reg.mgz --targ tp1_t1_reg.mgz for time-point 1, etcetera. Stefano [Freesurfer] Longitudinal SAMSEG with multi-contrast data<https://secure-web.cisco.com/1wqAljGN-HfqNgjoB_GLYISZdkqc0_9NrBWKfoyXxioxHK…> Gonzalo Rojas Costa<https://secure-web.cisco.com/17xEk5nL7zi1KleESqeBlN3BTHFcZZZ5aIVXY_BJb6V_Lk…> Mon, 12 Jun 2023 10:21:51 -0700<https://secure-web.cisco.com/1emebkgy5p75OaE8PVfVUI7Bh8WG2NzT6RocEeQ_clhqM6…> External Email - Use Caution Hi: How can I generate "tp1_flair_reg.mgz" image appeared in command "run_samseg_long --timepoint tp0_t1_reg.mgz tp0_flair_reg.mgz --timepoint tp1_t1_reg.mgz tp1_flair_reg.mgz --timepoint tp2_t1_reg.mgz tp2_flair_reg.mgz --output outputDir/" ? Sincerely, Gonzalo Rojas Costa _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1gm8Mo90Xz5BNWI2qCZ6Q3l2guFyqznXM3Mc10zV67LMsh… 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/12Agmx53cqZKs72ZRcgmLh2khJsG4EHKL-2xt0JtfedpJH… <https://secure-web.cisco.com/12Agmx53cqZKs72ZRcgmLh2khJsG4EHKL-2xt0JtfedpJH…> . 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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Longitudinal SAMSEG with multi-contrast data
by Gonzalo Rojas Costa 12 Jun '23

12 Jun '23

External Email - Use Caution Hi: How can I generate "tp1_flair_reg.mgz" image appeared in command "run_samseg_long --timepoint tp0_t1_reg.mgz tp0_flair_reg.mgz --timepoint tp1_t1_reg.mgz tp1_flair_reg.mgz --timepoint tp2_t1_reg.mgz tp2_flair_reg.mgz --output outputDir/" ? Sincerely, Gonzalo Rojas Costa

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VM password
by Chad Haines 12 Jun '23

12 Jun '23

External Email - Use Caution Hello. I would like the password to the Ubuntu VM that has Freesurger installed on it. Thank you.

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Generate Stats File for fornix.mgz in T1 weighted MRI ?
by Ahsan Ali 12 Jun '23

12 Jun '23

External Email - Use Caution Dear Sir/Madam, I'm having a ADNI T1 weighted MRI database. I have run the recon-all command successfully and got a couple of default stats files in the stats folder. Then fornix.mgz is estimated using command "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto_CCseg.mgz -f folder_name" successfully. Now what can be done to generate the stats for fornix.mgz? I've been struggling with this for a long time, please help me with this. I'm using ubuntu. [image: IMG-20230526-WA0000.jpg] With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552

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trac-all ERROR: Option syn/acomm.flt.prep.trk unknown
by Stylianos Charalampous 12 Jun '23

12 Jun '23

External Email - Use Caution Hello, I am attempting to run white matter tractography using TRACULA, as described in the tutorial, however, using a brain parcellation acquired using an external algorithm. I have put the aparc+aseg.mgz file in the subject directory in folder mri but I am getting the following error: ERROR: Option syn/acomm.flt.prep.trk unknown Linux GS63VR-6RF 5.19.0-43-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon May 22 13:39:36 UTC 2 x86_64 x86_64 x86_64 GNU/Linux I also get the following error in the start of the prior fitting step in case they are linked: #@# Priors Mon Jun 12 11:43:04 AM BST 2023 error: Could not create temporary file in /tmp $slistfile: Ambiguous. The error occurs when running the prior calculation step using the prep command: trac-all -c config_file -prep. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this one? 1) FreeSurfer version: freesurfer-7.3.2 2) Platform: ubuntu-22.04.02

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Huge difference between volumes for Freesurfer vs CAT12
by Michael Mc Laughlin 10 Jun '23

10 Jun '23

External Email - Use Caution I have used both CAT12 and Freesurfer to segment a particular brain scan and I get completely different volumes. CAT12 (cc) Freesurfer 7.3.2 (cc) Left Cerebral White Matter volume(cc): 209 Left hemisphere cerebral white matter volume 242 Left Cerebral Cortex volume(cc): 444 Left hemisphere cortical gray matter volume 269 Left Lateral Ventricle volume(cc): 28 Left-Lateral-Ventricle 43 Right Cerebral White Matter volume(cc): 208 Right hemisphere cerebral white matter volume 242 Right Cerebral Cortex volume(cc): 440 Right hemisphere cortical gray matter volume 270 Right Lateral Ventricle volume(cc): 20 Right-Lateral-Ventricle 28 Total 1350 Total 1095 Total volume (cc): 1618.09 Brain Segmentation Volume 1309 Estimated Total Intracranial Volume 1852 What could be causing this difference? The brain scan was done with MPRAGE protocol with 176x256x256 voxels of size 1mmx0.976mmx0.976mm Which one is correct? The scan is of a normal adult male aged 62 with chronic migraine. Michael McLaughlin,

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Freesurfer June 2023