Freesurfer September 2022

freesurfer@nmr.mgh.harvard.edu

92 participants
129 discussions

Re: [Freesurfer] Error
by fsbuild 23 Sep '22

23 Sep '22

External Email - Use Caution Hello Ahmed, Command terminated by signal 9 can mean you ran out of memory.  I would try allocating more memory to the VM.  But you may still run out of memory depending upon what is available on your machine. If you do not have to use 7.1.1 and can switch to using the newer 7.3.2 release, then for Ubuntu 20, we have a .deb file installer (https://secure-web.cisco.com/1X7NA_6gOlCGu2ju8c-dGWtwYTkO0F2UyQn6LX3rWhDeWj… or a tar archive (https://secure-web.cisco.com/1UYiwKeazHITmgtErAJKToWU57RsDIl-czevJWE_lnANvB…) which you try.  I would uninstall 7.1.1 if you are going to use 7.3.2 though.  Again, that may not help if available memory is the issue. - R. On Sep 23, 2022, at 02:04, Ahmad Khan <110ahmadkhan(a)gmail.com> wrote:        External Email - Use Caution         Dear Free Surfer Development Team.I am using the recon -all command to compute the volume of different regions of the brain. I am running the free surfer version freesurfer-linux-centos7_x86_64-7.1.1-20200723 on Ubuntu 20.4 installed on a virtual box. I am getting the following errors and the log file is also attached with this email. ERROR: mri_ca_register with non-zero status 137Your timely response would be highly appreciated.Best Regards Dr. Ahmad Raza Khan(Ramalingaswami Fellow)Center of Bio-Medical Research (CBMR)SGPGI Campus, Raibareli RoadLucknow-226014, UP, INDIA<recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Running v7 with recon-all v6 files
by fsbuild 23 Sep '22

23 Sep '22

External Email - Use Caution Hello Alexandra Please let us know if you are on an Intel or a newer Mac with an arm processor, e.g., M1, M2 chip.  You could send along a screen shot of what "About this Mac" displays. Per the "Important Note" at the bottom of the freesurfer release page, https://secure-web.cisco.com/1bbOhG1CjL59gEStW3FxyyS6evApjdBtrtnRNMXkTQqF0f…, you may not get exactly the same (floating point) results when running v6 on a different/newer version of MacOS. - R. On 9/22/22 09:36, Alexandra Brouillard (brouillard.alexandra(a)gmail.com) wrote:         External Email - Use Caution         Hi   I ran recon-all on an external server using the version 6. I recently downloaded the v6 on my Mac v12.6. I was able to set a home directory but get a ‘permission denied’ error when typing ‘$FREESURFER_HOME’ (but have the permissions/sudo). I also can’t open Freeview: by double clicking on the app, the GUI crashes, or by typing ‘freeview’ in the terminal I get a PETSC error.  According to some previous forum threads, I’m thinking of downloading the v7 but would like to validate that it’s OK when using recon-all v6 files.   Thank you for your support,   Alexandra   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1wXMF-HNnKPbJ6UCMl7zjaYS6CvQ0xP-EjJ9WxjSWmuVhO… 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/1bQ9M6iur_iW-pPNsqXlrhmaSi_R4XGPHVen9gzb4NtkW_… <https://secure-web.cisco.com/1QEu65hJzFz0Qlr-f85ovtCCFPcEQTuVjkATuX8Dzuz3-aNImRz08NXygo1pKr2Wbp8Y7ERP6XX_QXuwwA7OQtL95Jy8KMvQkj8V15v6C3snSGsuYEymHIorCwk50lasrKb8M0DVESSb7lpsfhGW7Z8XrutrhY2vETqwYjoknqZ2L7coJdB9m0JwsRPxH88FkJaPyuapnujCIKZ0QiH7JLW_PxPUN1xjG8C0rI2ClwPd8PHXFdDo4ft_5ujxHY0YquA5UdKOwf3hc1himt1m2KKha9Xl8cwmMraWndDu5-S3ei8hubimZcdWjlXmybq7wVZ40Jt_OHoyghzrMyO1mZg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . 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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Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu
by fsbuild 22 Sep '22

22 Sep '22

External Email - Use Caution I can check to see if there is a license in the Freesurfer v5 Ubuntu VM I mentioned in the previous email and send it to you to try.   But per my last email, I don’t know a way to decode an old license on newer versions of the OS where glibc has been updated short of re-compiling what decodes the license.   The most practical option may be to run FS 5.3 on a server that hosts an old version of Ubuntu that works with your existing license.   That can be done using a headless VM or container where the image runs off an SSD with a hefty amount of RAM assigned to it.  Ubuntu supports QEMU virtualization like most linux OS’s and I think you just install those packages from the linux repos.  For commercial software, VMware has enterprise level server hosting options for these kinds of tasks. - R. On Sep 22, 2022, at 06:25, Caspar Schwiedrzik <cschwiedrz(a)mail.rockefeller.edu> wrote:        External Email - Use Caution        Hi! Would it be possible to obtain a license file for Freesurfer v5.3 that is compatible with the glibc versions on newer Linux systems? That would go a long way in resolving our issues. Thank you, Caspar _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer

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Longitudinal PET analysis
by Gomar, Jesus 22 Sep '22

22 Sep '22

External Email - Use Caution Hello Freesurfer developers, I am interested in analyzing PET data following a longitudinal design. I have co-registered each PET image to the closest MRI in time processed through the longitudinal stream. I have sampled each co-registered PET image time-point onto fsaverage surface via the individual's subject surface (mri_vol2surf). >From this point: 1. Is it possible to obtain spc (symmetrized percent change) using long_mris_slopes for each subject? 2. Is there a way to input the sampled surfaces into a qdec file for long_mris_slopes command? 1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.2.0. 2) Platform: Ubuntu 18,04.6 LTS 3) uname -a: Linux ubuntu 5.4.0-122-generic-Ubuntu UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Thank you! Jesus The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu
by Caspar Schwiedrzik 22 Sep '22

22 Sep '22

External Email - Use Caution Hi! Would it be possible to obtain a license file for Freesurfer v5.3 that is compatible with the glibc versions on newer Linux systems? That would go a long way in resolving our issues. Thank you, Caspar

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Three year postdoctoral fellowship in large-scale neuroimaging of thalamus and brainstem nuclei in brain disorders at the Norwegian Centre for Mental Disorders Research (NORMENT)
by Stener Nerland 22 Sep '22

22 Sep '22

External Email - Use Caution NORMENT runs a multicenter study involving hospital departments in Oslo and several research groups at the University of Oslo. The purpose of the programme is to study how biological/genetic, psychological and environmental factors contribute to mental and other brain disorders. We pursue diversity among our job applicants and encourage everyone to apply regardless of who you are and what background you have. Duties and responsibilities: Novel magnetic resonance imaging (MRI)-based tools will be used to investigate the structure of individual thalamic and brainstem nuclei in a large in-house multi-site sample of healthy controls (HCs; N>38,000) and participants with common brain disorders (N>5,900), including schizophrenia (SCZ; N>1,100) and bipolar disorders (BD; N>450). To determine how the thalamic and brainstem nuclei alterations affect cortical functioning, we will obtain electroencephalography (EEG)-based indices of cortical synaptic function and cortical oscillatory activity from patients and HCs with MRI (N>650). The overall goal of the study is to advance our understanding of 1) whether individual thalamic and brainstem nuclei are altered in common brain disorders, 2) how the nuclei alterations affect cortical functioning, and 3) if these alterations link to clinically relevant subgroups. The successful candidate will analyze and publish already collected clinical and MRI data and contribute to the ongoing data collection. Qualifications: Successful applicants must hold a PhD degree in neuroscience or equivalent, document experience in neuroimaging-based research, preferably from MRI- or EEG-based projects. Strong analytical and problem solving skills and attention to details are desirable. Personal skills will be emphasized. The candidate should be able to work independently and interactively in a team setting, be motivated and responsible, and be passionate about research. We can offer: An exciting research environment with a multidisciplinary profile and great opportunities for academic development. Attractive welfare and pension arrangements and a salary level in accordance with qualifications. For more information and to submit an application, please follow this link to the job announcement: https://secure-web.cisco.com/1yc_HfEpKe3vd6nOQKOBMCR6VMhZ8_qV6S4p8aHl4NWWOV…

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pass code virtual machine Free Surfer
by Luisa Klahn 22 Sep '22

22 Sep '22

External Email - Use Caution Hi, I am installing the virtual machine to run Free Surfer on my windows computer and I need the pass code to open the 7zip files archive. Can someone please send that to me? Thank you very much! Best, Luisa Klahn

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Voxel to mm coordinates
by Fotiadis, Panagiotis 21 Sep '22

21 Sep '22

External Email - Use Caution Hello, I was wondering what the best way would be to extract the coordinates of each voxel in my nifti volume in mm. I have used MRIread to load the nifti volume into Matlab (=mri) and wanted to essentially create a new variable that takes each (voxel) entry in mri.vol and exports its three coordinates in mm. Would I just need to multiply the mri.vox2ras 4x4 matrix to each voxel’s [X Y Z 1]’ (where X,Y,Z are the voxel’s coordinates in mri.vol) or are there different steps involved? Thank you in advance for your time and help! Best, Panos

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unziping problems
by TAIB Simon 21 Sep '22

21 Sep '22

External Email - Use Caution Good afternoon, I am having trouble unzipping the freesurfer folder downloaded from your website as a password is required and I could not find it. I have done my registration and got the licence.txt file, but I don't know if the password is in it. Is there something I am missing ? If so, please enlight me. Have a good day Dr Simon TAIB Centre Régional Psychotraumatisme Occitanie - CHU de Purpan INSERM U1214 ToNIC - Université Toulouse 3 ________________________________ Ce message et les éventuelles pièces jointes sont confidentiels et peuvent être protégés par la loi. Ils s'adressent uniquement aux personnes destinataires. Si vous n'êtes pas dans la liste des destinataires, veuillez en informer immédiatement l'expéditeur et ne pas utiliser, divulguer, stocker ou copier sur un quelconque support l'information qu'il contient. Il appartient au destinataire de vérifier que les messages et pièces jointes ne contiennent pas de virus. This message and any attachments are confidential and may be protected by law. They are intended only for the individual(s) or entity named above. If you are not the intended recipient, any disclosure, copying, or distribution is strictly prohibited. Please notify the sender that you have received this email by error. It belongs to each recipient to check that e-mails and attachments are free from viruses.

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Unable to run trac-all -prep : cannot file bvals bvecs file
by Ashwati Vipin (Dr) 20 Sep '22

20 Sep '22

External Email - Use Caution Dear Freesurfer developers, I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error: writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz... /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt: No such file or directory. Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022 I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I’m not sure why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work. [cid:image001.png@01D8B09D.94718010] I have run tracula before with no issues so I’m really lost here. Could you please help? Thank you so much! Best, Ashwati ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

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Freesurfer September 2022