Freesurfer July 2023

freesurfer@nmr.mgh.harvard.edu

93 participants
130 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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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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Code not working
by Rachel Wagner 31 Jul '23

31 Jul '23

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

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Re: [Freesurfer] Freesurfer version and Installation
by fsbuild 31 Jul '23

31 Jul '23

External Email - Use Caution Development builds are continually updated and may not be stable, i.e., so the March 31st development build is no longer available.  I suggest using one of the release builds listed on the release page.  The 7.4.1 build from this June is the most recent release there with download links. - R. https://secure-web.cisco.com/1mozD5gXusZi5ReWhcLJuHVCFslf2OLCNdFPx2ADAwbvA7… On Jul 31, 2023, at 14:38, hmarzban(a)student.ubc.ca wrote:        External Email - Use Caution        Dear Freesurfer developers,Previously, I downloaded the freesurfer-linux-centos7_x86_64-dev-20230331-e304091 version and successfully analyzed some data using this version. Now, I find myself in the need to reinstall Freesurfer, but I am unable to locate the source file on your website.Could you kindly guide me to where I can find the mentioned version? Alternatively, if this specific version is no longer available, please advise me on which version I should download and install to achieve the same results as before.Thank you very much for your assistance.RegardsHengameh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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(no subject)
by Atwater, Emanuel R 31 Jul '23

31 Jul '23

External Email - Use Caution Hello FreeSurfer Team, I recently messaged about running a longitudinal scan on a couple of images. The response told me to utilize "timepoints": For base processing, specify each timepoint with -tp <> (not the nii file). recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all I've attempted to review the youtube videos and instructions made available online but am unsure what "timepoints" are. Can I have some clarification on what exactly a timepoint is, please. FS version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b Recon-all.log: see attached V/r, Emanuel Atwater

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Freesurfer July 2023