Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Bigventricles segmentation
by Goodheart, Anna E.,MD, MSC 08 Oct '24

08 Oct '24

Hi FreeSurfer Team, I’m following up on a previous archived thread about trying to fix the segmentation of a scan with very large ventricles. Unfortunately, even with the -bigventricles flag I have a scan in which the posterior lateral ventricles are being included as white matter, and most of the corpus callosum is not being recognized. I tried editing the wm.mgz file without success. I’m using version 7.2.0. I’m happy to share images if helpful, or physically show someone if possible (I’m located in Building 149). Thank you very much! Anna -- Anna Goodheart, MD, MSc Massachusetts General Hospital Department of Neurology

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Freeview error with QT
by Eashrat Muniya 08 Oct '24

08 Oct '24

External Email - Use Caution Dear all, i am facing this issue with QT but i am sure i have put all the environment variable for QT correctly. Can someone help me solve this issue? In the end I want to use the Synthseg. Any help is appreciated! Thanks! Regards Eashrat [cid:d7714658-35e6-49b4-aced-eb50fccb03d7]

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NIH funded postdoc position at Child Mind Institute
by Ting Xu 08 Oct '24

08 Oct '24

External Email - Use Caution Child Mind Institute is recruiting a Post Doctoral Fellowship interested in the study of brain structure and function connectome using multimodal neuroimaging techniques. Particular focus will be placed on brain development and cross-species comparison between human and nonhuman primates based on both in vivo and ex vivo MRI imaging data. This is an exempt full-time position (2-3 years) located in our New York headquarters office. Responsibilities: • Development, application, and refinement of analytic approaches for multimodal data, including, but not limited to, functional and structural imaging data. • Preprocess of functional and diffusion MRI datasets in human and nonhuman primates on high-performance computing infrastructures. Develop scientific-quality tests for evaluating the results of cutting-edge brain imaging analysis pipelines • Extend processing techniques used in analyzing brain imaging data and evaluate/compare novel approaches to the state-of-the-art in brain imaging research. • Preparation of manuscripts for publication in peer-reviewed scientific journals and assistance in grant applications in a timely fashion • Preparing data to be shared with research collaborators for experimentation and publication. • Assistance in the supervision of junior research staff (e.g., research assistants, data analysts) Qualifications: • Completed PhD in neuroscience, biomedical engineering, computer science, mathematics, biophysics, neuropsychology or related fields. • Significant prior neuroimaging experience with one or more imaging modalities (fMRI, DTI, MRI, EEG, MEG) • Strong skills in using one or more common functional neuroimaging packages (e.g., AFNI, FSL, FreeSurfer, SPM, etc.) • Strong programming experience in one or more languages (e.g., Python, R, Matlab etc.). • Ability to work as a member of a team as well as independently • Ability to work in a fast-paced environment • Interpersonal skills, as well as written and oral communication • A passion for the Child Mind Institute's mission For more information and apply, please visit: https://secure-web.cisco.com/1m0dzu-E1-XWjr-LWM70d-qHt3lOHzpu3awku2gpiDTwUn… If any questions, please reach out to the PI, Ting Xu (ting.xu(a)childmind.org ).

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Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer
by fsbuild 08 Oct '24

08 Oct '24

External Email - Use Caution Please send along a screenshot of what you see when you select from the upper right hand corner Apple pull down menu —> About this Mac.   You may not have the resources to run some of the python commands. After you setup the fressurfer shell environment, please send along the output from these commands in the terminal window,$ which python<your output>$ python --version<your output> - R. On Oct 7, 2024, at 16:54, Johnson, Ian <ian.p.johnson(a)yale.edu> wrote:        External Email - Use Caution        I am running Sequoia 15.0.1.From: fsbuild <fsbuild(a)contbay.com> Sent: Monday, October 7, 2024 4:36 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer  Please let us know the operating system name and revision running on the machine. - R. On Oct 7, 2024, at 16:13, Johnson, Ian <ian.p.johnson(a)yale.edu> wrote:        External Email - Use Caution        Hello Free Surfer Pros, I am trying to run WMH-Synth-Seg on a different machine (2.4GHz Quad-Core Intel Core i5, Intel Iris Plus Graphics 655 1536 MB). I am getting the error message: "line 30: /Applications/freesurfer/dev/python/bin/python3: Bad CPU type in executable" Is this machine too old to run WMH FreeSurfer? Best,Ian Johnson, B.A.Clinical Research AssociateDivision of Neurocritical Care & Emergency NeurologyYale School of MedicineE: ian.p.johnson@yale.edu_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_WMHsynthseg error: Killed 9
by Johnson, Ian 07 Oct '24

07 Oct '24

External Email - Use Caution Hello SynthSeg Experts, I am having an issue when I run mri_WMHsynthseg. I have run the program many times before without any issues. I recently closed my terminal while updating my Mac and reopened it to run WMHsynthseg. I have seen from previous posts that the "killed" error is because of an issue with RAM, but I have not run into this error in the past. The error occurs while on the "Pushing data through the CNN" step. There is no error message, terminal just prints "killed: 9" Best, Ian J

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Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer
by fsbuild 07 Oct '24

07 Oct '24

External Email - Use Caution  Please let us know the operating system name and revision running on the machine. - R. On Oct 7, 2024, at 16:13, Johnson, Ian <ian.p.johnson(a)yale.edu> wrote:        External Email - Use Caution        Hello Free Surfer Pros, I am trying to run WMH-Synth-Seg on a different machine (2.4GHz Quad-Core Intel Core i5, Intel Iris Plus Graphics 655 1536 MB). I am getting the error message: "line 30: /Applications/freesurfer/dev/python/bin/python3: Bad CPU type in executable" Is this machine too old to run WMH FreeSurfer? Best,Ian Johnson, B.A.Clinical Research AssociateDivision of Neurocritical Care & Emergency NeurologyYale School of MedicineE: ian.p.johnson@yale.edu_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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error: Bad CPU type in executable WMH FreeSurfer
by Johnson, Ian 07 Oct '24

07 Oct '24

External Email - Use Caution Hello Free Surfer Pros, I am trying to run WMH-Synth-Seg on a different machine (2.4GHz Quad-Core Intel Core i5, Intel Iris Plus Graphics 655 1536 MB). I am getting the error message: "line 30: /Applications/freesurfer/dev/python/bin/python3: Bad CPU type in executable" Is this machine too old to run WMH FreeSurfer? Best, Ian Johnson, B.A. Clinical Research Associate Division of Neurocritical Care & Emergency Neurology Yale School of Medicine E: ian.p.johnson(a)yale.edu

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tkmedit does not start
by Francesco Lomi 07 Oct '24

07 Oct '24

External Email - Use Caution Dear all, I am writing you because I am trying to launch tkmedit on my Ubuntu computer but the program does not start. I get no errors but simply the terminal goes back to a new input line. I have Freesurfer correctly installed because I normally use freeview and recon-all runs without problems. If you had any suggestions they would be highly appreciated Best, Francesco

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Re: [Freesurfer] Freesurfer stopped working after updating to Ubunto 24.04.1 LTS
by fsbuild 05 Oct '24

05 Oct '24

External Email - Use Caution Hello Raj, Sometimes when OS’s update to a new major revision, the system libraries change such that software installed under the old OS version is not backwards compatible with the new OS version.  I think we may have already mentioned on the list that the current freesurfer builds/releases do not yet support installing or running on Ubuntu 24.  VM applications like Oracle’s VirtuaBox, and those from VMware, etc., support making a snapshot and/or backup copy of the VM’s disk image..  So for example, before upgrading from Ubuntu 22 to Ubuntu 24 you could clone the current VM  (as VirtualBox calls it) so that you have a copy (or a 2nd) VM that is your old Ubuntu 22 system.   You just need to have enough disk space to store snapshots and/or clones/backups of the virtual machine.  Sorry I don’t have a workaround to run 7.4.1 on Ubuntu 24. - R. On Oct 5, 2024, at 06:26, Raj Agarbattiwala <raj27289(a)gmail.com> wrote:        External Email - Use Caution        Dear Developers I installed Freesurfer 7.4.1 when using Ubuntu 22 in an Oracle VM on Windows 10 as a host OS. However, I recently updated to Ubuntu 24.04.1 LTS (I still regret it), and after that, Freesurfer stopped working. It shows "bash: /usr/local/freesurfer/7.4.1/ SetUpFreeSurfer.sh: No such file or directory" as an error message. I tried to re-install Freesurfer, and it showed the following error message: The following packages have unmet dependencies: freesurfer : Depends: libncurses5 but it is not installable Depends: libc6 (< 2.36) but 2.39-0ubuntu8.3 is to be installed E: Unable to correct problems, you have held broken packages. I am a Neurosurgeon in Mumbai. I have beginner-level knowledge of programming. Please help me out. Regards Raj Agarbattiwala Jaslok Hospital and Research Center, Mumbai_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/11xpk6NwlTzyo7_bufXgr7-1Uj_QbwYQSmscCI2OEi7z2i…

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Freesurfer stopped working after updating to Ubunto 24.04.1 LTS
by Raj Agarbattiwala 05 Oct '24

05 Oct '24

External Email - Use Caution Dear Developers I installed Freesurfer 7.4.1 when using Ubuntu 22 in an Oracle VM on Windows 10 as a host OS. However, I recently updated to Ubuntu 24.04.1 LTS (I still regret it), and after that, Freesurfer stopped working. It shows "bash: /usr/local/freesurfer/7.4.1/ SetUpFreeSurfer.sh: No such file or directory" as an error message. I tried to re-install Freesurfer, and it showed the following error message: The following packages have unmet dependencies: freesurfer : Depends: libncurses5 but it is not installable Depends: libc6 (< 2.36) but 2.39-0ubuntu8.3 is to be installed E: Unable to correct problems, you have held broken packages. I am a Neurosurgeon in Mumbai. I have beginner-level knowledge of programming. Please help me out. Regards Raj Agarbattiwala Jaslok Hospital and Research Center, Mumbai

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