Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Grey Matter Under Segmentation
by Fatima Abboud 01 Aug '23

01 Aug '23

External Email - Use Caution Hello, I have run FreeSurfer v7.1.1 on the CBRAIN platform and I'm performing QC on the output using the information at the following page: https://secure-web.cisco.com/1oUroAUDs4KHQ2Dm_LBBIXd9QC0wayhlpqddWcLfLv3VRD… It seems though that for almost all of my output, a large portion of the grey matter is not being segmented (please see attached example). I'm not sure if there is a solution to this or if the images will just need to be manually edited to fix this under segmentation. I would greatly appreciate any help or insight. Thank you for your time and help, Fatima

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Longitudinal base error
by Bernis SÜTÇÜBAŞI 01 Aug '23

01 Aug '23

External Email - Use Caution Hello FreeSurfer experts, I'm attempting to follow the longitudinal pipeline, as described on the longitudinal processing tutorial (https://secure-web.cisco.com/1vfvhhwIW62eUqagABMhB_WTdPL428NuWWIuhlLA1wrade…) while creating a within-subject template, I get the following error when I run this command: recon-all -base Subj03_template -tp /Users/bernis/Calismalar/results/Subj03/Subj03_TO/Subj03_TO.nii -tp /Users/bernis/Calismalar/results/Subj03/Subj03_TS/Subj03_TS.nii -all error: mghRead(/Users/bernis/Calismalar/results/Subj03_TS.nii/mri/rawavg.mgz, -1): could not open file Does anyone have any idea how I can resolve this problem? 1) FreeSurfer version: v7.2.0 2) Platform: MacOS Big Sur release 11.6.7 3) recon-all.log: see attached Best regards, [https://secure-web.cisco.com/1FcV40hswwSeEl9bym6WfCPck8eyt1yR9LF87hH45tP9co…]<https://secure-web.cisco.com/1gg-VeXoq9W6DUMYRFkUMcIADYHC7qN0RuiQhEnLA0K-N7…> Bernis Sütçübaşı Assist. Prof. Faculty of Humanities and Social Sciences/Department of Psychology Kerem Aydınlar Kampüsü Kayışdağı Cad. 32 Ataşehir 34752 İstanbul Tel 0 216 500 36 05

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Registration open: FSL Course 2023 - Sept 11th-22nd
by Rezvan Farahibozorg 01 Aug '23

01 Aug '23

External Email - Use Caution Dear all, Registration is now open for FSL Course 2023, which will be held fully online, 11th - 22nd September 2023. You can find details and registration info here: https://secure-web.cisco.com/1cIeIiYp0f3jnyTe1eIgI6q513zNQxlZqiN1b6AYIFmgLg… To strike a balance between broad accessibility and the benefits of in-person interaction, the FSL Course intends to follow an approximately alternating pattern of fully in-person and fully online courses. The only option to attend the course in 2023 will be this online course. Both new and existing users of FSL are welcome on the course, as it aims to cover both basic and more advanced features of FSL! The course covers the theory and practice of functional, structural, diffusion and resting state brain image analysis, with recorded lectures and live practical sessions where attendees learn how to carry out analysis for themselves on real data, with access to experienced tutors available throughout each session. In order to accommodate different time zones, there will be two parallel courses repeating the same content. Each session will consist of a self-paced practical, with guidance available from our expert tutors via Zoom (or equivalent), and all FSL software and course data pre-installed and ready to go on a cloud-enabled virtual desktop. All lectures will be pre-recorded and available as video podcasts, and speakers will be available for questions and discussions. You would need your own computer/laptop/tablet that can do video conferencing and host the remote desktop client, as well as a reasonable internet connection that is good enough for video conferencing. If your institute is at a low/middle income country, you will also be able to request a discount, as instructed on the registration page. We hope to see you at the course! The FSL Course team

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mris_preproc error: cannot allocate memory
by MANSSOUR Wassima 01 Aug '23

01 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I'm conducting the Surface Based Group Analysis explained on the FStutorial GroupAnalysisV6.0, but I keep getting the error: "Cannot allocate memory" while running the mris_preproc command. I'm using the data of 355 subjects stored on an external hard drive, and a pc of 23G RAM, but it stops at the 334 subject. I've already tried with a windows and mac of 16G RAM and got the error, so moved to the other one but still getting the same issue. Does anyone have any thoughts on how to trouble-shoot this? or any other alternative solution to run the mris_preproc on all the subjects? FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platforme: Debian 3.16.7 Thank you for your help, -- Wassima MANSSOUR Master Student at INSEA Rabat M2SI - Information Systems & Intelligent Systems IMRB Intern-France wmanssour(a)insea.ac.ma<mailto:wmanssour@insea.ac.ma> wassima.manssour(a)u-pec.fr<mailto:wassima.manssour@u-pec.fr>

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Re: [Freesurfer] MAC OS Ventura problems
by fsbuild 31 Jul '23

31 Jul '23

External Email - Use Caution  Try right clicking on the .pkg installer and select “open with” and then select “installer.app”.  That should allow you to do an install of the distribution which will go under /Applications/freesurfer/7.4.1, e.g., for the 7.4.1 release pkg obtained via the link,  https://secure-web.cisco.com/1Ykhf9FuCkslH36IMqiGn4EMsGDCmsjO4PjpHzy0g-46r2… You will need to set SUBJECTS_DIR to some other path not under /Applications where you can normally write to as your userid, e.g.,  $ mkdir $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects - R. On Jul 31, 2023, at 18:16, Alan Francis <alandarkenergy(a)gmail.com> wrote:        External Email - Use Caution        Hi Doug et al,I recently moved from Linux to MAC OS running Ventura.. When I run the recon-all, it gives me this message:“mri_compute_overlap” cannot be opened because the developer cannot be verified.The help given at the FS website is for previous MAC versions. Ventura does not allow what is shown on the website.Any suggestions?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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Unable to read in images from Freeview command window
by Rachel Wagner 31 Jul '23

31 Jul '23

External Email - Use Caution Hello, I am looking to cortically project onto a pial surface and am trying to use the following code in the freeview GUI to do so: [FreeView] -v 004/mri/wm.mgz:colormap=jet 004/mri/brainmask.mgz -f 004/surf/lh.pial:edgecolor=blue 004/surf/lh.white:edgecolor=red error: mghRead(/home/developer/freesurfer/004/mri/wm.mgz, -1): could not open file MRIread failed: Unable to read from /home/developer/freesurfer/004/mri/wm.mgz I don’t know how to resolve this, any guidance would be greatly appreciated. Thank you, Rachel Wagner

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Remove border vertices
by Marina Fernández 31 Jul '23

31 Jul '23

External Email - Use Caution Dear experts, I would like to project a parcellation (annot file) onto the cortical surface removing or hiding the border vertices of the different labels of the parcellation. I thought that I can do that scripting but first I would need to know which vertices are border vertices. Or is there a simpler way to do it? Thank you very much in advance. Bets regards, Marina

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MAC OS Ventura problems
by Alan Francis 31 Jul '23

31 Jul '23

External Email - Use Caution Hi Doug et al, I recently moved from Linux to MAC OS running Ventura. When I run the recon-all, it gives me this message: “mri_compute_overlap” cannot be opened because the developer cannot be verified. The help given at the FS website is for previous MAC versions. Ventura does not allow what is shown on the website. Any suggestions? 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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infantFS download
by Katie Rose Jobson 31 Jul '23

31 Jul '23

External Email - Use Caution Hi FS experts, I was just wondering about how long it takes to receive the download for infantFS. I would like to use the program to analyze my dissertation data, so I just want to have a timeframe in mind for about how long it will take to start to use it! I have already requested the code, so hopefully I am not missing anything. Thanks so much for your help! Best Wishes, Katie -- Katie Jobson, M.S. | Personal Website<https://secure-web.cisco.com/10_j6t2N0K4j4O9iJsbNnZzFZ6KjmMsAK-syQjc-l05q5s…> Board Member | Coding Outreach Group<http://secure-web.cisco.com/12Zi_WQIrRPgQECahTGwWQfzfrdY2tem_74h9tp1EUP85hG…> Ph.D. Student | Cognitive Neuroscience Lab<https://secure-web.cisco.com/1w8iwMoXD5YPirkI4qk0v833_wA_XAfDJOIHsqt13EPdTF…> Department of Psychology and Neuroscience | Temple University

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Re: [Freesurfer] Code not working
by fsbuild 31 Jul '23

31 Jul '23

External Email - Use Caution  It reads like you downloaded and setup the public VM (from https://secure-web.cisco.com/1YpN3buNDQ0c9lVvFb2LEMMoXu4bGzcQrSQ6…) and had it working ? If so, as shown by the screenshot at the bottom of that web page, the freesurfer environment is already setup by default when a new terminal window opens (and in that screenshot is using bash but not csh/tcsh).  You should not have to be setting the environment variables by hand as they appear listed at the top of the screenshot of the terminal. If your $HOME/.bashrc file was edited/changed, or you changed the default shell from bash to csh/tcsh, then it’s possible that setup is no longer working. If you accepted one of the prompts to *upgrade* the system to a newer version of Ubuntu, then the setup may no longer be working. For the public VM, this file should list you are running Ubuntu 18.04 $ cat /etc/os-release NAME="Ubuntu"VERSION="18.04.6 LTS (Bionic Beaver)"ID=ubuntuID_LIKE=debianPRETTY_NAME="Ubuntu 18.04.6 LTS"VERSION_ID=“18.04”… rest of output deleted ... If your system was upgraded it will probably say Ubuntu 20. - R. On Jul 31, 2023, at 16:31, Rachel Wagner <rwagne2(a)uwo.ca> wrote:        External Email - Use Caution        Hello all,  I’m getting an error as follows: developer@developer-VirtualBox:~/freesurfer$     setenv SUBJECTS_DIR $FREESURFER_HOME/subjects Command 'setenv' not found, did you mean:   command 'getenv' from snap getenv (0.3.1) See 'snap info <snapname>' for additional versions. developer@developer-VirtualBox:~/freesurfer$   Is something not installed? These functions were working previously. Thanks, Rachel_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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