Freesurfer

freesurfer@nmr.mgh.harvard.edu

13 participants
30061 discussions

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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Freeview ERROR: label name '3rd-Ventricle' is duplicated
by Ha Manh Luu 31 Jul '23

31 Jul '23

External Email - Use Caution Hello FreeSurfer Developers, I have installed FreeSurfer v6.0.0 in my MacOS 12.6.7 but I got Freeview crashed due to PETSC error (which has been fixed in FreeSurfer v7.1.1). https://secure-web.cisco.com/1ZFMUj_7IrIwJpKg8t9MDv8HXjMl4zkUnvbZXAYynkbCwx… For the consistency to my previous work, I do not want to upgrade to Freesurfer V7.X in my MAC. I updated freeview from this website: https://secure-web.cisco.com/1S9x5E_CG-W__zwFRdlOGUd46esEXWkTVTFNdMWvd8QFAt… After updating, Freeview works for me but it still shows the following error: ERROR: label name '3rd-Ventricle' is duplicated! ERROR: label name '3rd-Ventricle' is duplicated! CTABfindDuplicateNames: 1 duplicate names found in: /private/var/folders/4w/c9v2n39j3hd_4rb1bmyrftqw0000gt/T/FreeSurferColorLUT.txt I cat the file and see that '3rd-Ventricle' has 2 lablels in the file. I also see that the FreeSurferColorLUT.txt file is not identical to the FreeSurferColorLUT.txt in FreeSurfer home folder. Can you tell me what is the file FreeSurferColorLUT.txt for and the issue is serious or not? If so, how to fix this. 1. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: MacOS Darwin 12.6.7 1. freeview: ERROR: label name '3rd-Ventricle' is duplicated! ERROR: label name '3rd-Ventricle' is duplicated! CTABfindDuplicateNames: 1 duplicate names found in: /private/var/folders/4w/c9v2n39j3hd_4rb1bmyrftqw0000gt/T/FreeSurferColorLUT.txt 2. FreeSurferColorLUT.txt: see attached Thanks, Ha

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Command not found
by Rachel Wagner 31 Jul '23

31 Jul '23

External Email - Use Caution Hello all, I have not used freesurfer in a couple of months, and have returned to create a new cortical projection image. I’m having an issue with my commands, they don’t seem to be recognized anymore and I’m not sure why: developer@developer-VirtualBox:~/freesurfer$ freeview Command 'freeview' not found, did you mean: command 'treeview' from deb treeview Try: sudo apt install <deb name> Is there any way to resolve this? Thanks, Rachel Wagner

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Password request for virtual machine installation
by Aaron S. 28 Jul '23

28 Jul '23

External Email - Use Caution Hello, just looking to get the password so I can unzip the virtual machine file 'FS_7_2_0_ubuntu_18_04_06.ova.zip' as per the instructions found here: https://secure-web.cisco.com/1ob4AXDbhbzqTxV6efnVHiFC74uJpjprhjdwl-BnfsqSh5… I recently got an MRI of my brain done and would like to 3D print a model for personal use. Thanks for your time!

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Passcode for virtual machine
by Noelle Abbott 28 Jul '23

28 Jul '23

External Email - Use Caution Hello, Can someone please provide me with the passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z ? Thanks, Noelle *~ ~ **~ ~ **~ ~ **~ ~ **~ ~ **~ ~ **~ ~ **~ ~ **~ ~ * *Noelle Abbott, Ph.D. Candidate* *SDSU/UCSD Joint Doctoral Program in Language and Communicative Disorders* *SLP Essentials Instructor* *Lab Manager, Language and Neuroscience Group, SDSU* *6505 Alvarado Rd, Ste 204San Diego, California 92120**Phone: 619.594.7878 * *https://secure-web.cisco.com/1bly9ydSxqTaYKuSFaH35yNknmiJLZ23JS3L_K2hsle1wsRjfr5cl0ucXbfnY0PQcMZ3_-u8MgkAmnYXTSzcwrU0CXJiVY9prBkGWpkRRttX9GExycg8lgeKeF-jKHbiVJQHiy2pPGFUVRBzhcsBVZLoRPiMWm1_vc0UXDEoPERDA12_HptApaJfGKhHhdyG5cXu3fmybMcsVA2jXwLXSaI7qkfyrIQtXPv0_Wwf0zRflSL38RRqQHHMpwf5-pAa87qUb-7fypGcxIaJAmUCHWORP4-5TsldZhR4zLoDk8ZjmWzCL2p3sSpiHQT3YqLwy3prn3MGC0XvxTmin7sMrvA/https%3A%2F%2Fslhs.sdsu.edu%2Flang%2F* <https://secure-web.cisco.com/1bly9ydSxqTaYKuSFaH35yNknmiJLZ23JS3L_K2hsle1ws…> <https://secure-web.cisco.com/1bly9ydSxqTaYKuSFaH35yNknmiJLZ23JS3L_K2hsle1ws…> *Pronouns: she/her/hers*

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PetSurfer, PET data format, mri_convert
by Zhou, Zeyu 28 Jul '23

28 Jul '23

External Email - Use Caution Hi Freesurfer developers, I am new to PET and FreeSurfer. I am trying to go through the PetSurfer tutorial (https://secure-web.cisco.com/1SgXjbJz8ibehnENjVYIj14hM83pSJC3l0yNLV0Ubo9CVp…) In Part 4 "Register your PET image with the anatomical", the PET data format in example is .nii.gz. However, here are the PET data I have (collected from SIEMENS HRRT PET): 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i.hdr 309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i 309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i.hdr 309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i 309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i.hdr 309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i 309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i.hdr 309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i 309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i.hdr 309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i 309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i.hdr I tried converting the .i file to (for example) an .nii file by mri_convert but got the following error message: mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i 309Fally0.nii ERROR: cannot determine file type for 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i Then I changed the .i file's extension to .img and the .i.hdr file's extension to .hdr and run mri_convert, but still got an error message: mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img 309Fally0.nii reading from 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img... error: ReadAnalyzeHeader: unsupported data type 17741 I couldn't find anywhere about how to process PET data in .i and .i.hdr files. Any suggestions? I attached one .i.hdr file for your reference. 1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 2) Platform: macOS Ventura 13.4.1 (c) 3) uname -a: Darwin rad-rsch-pc85 22.5.0 Darwin Kernel Version 22.5.0: Thu Jun 8 22:22:23 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T6020 arm64 Thanks. Best, Zeyu Zhou

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Postdoc position at MGH / Harvard Medical School: locus coeruleus connectomics of resilience
by Jacobs, Heidi (NP) 28 Jul '23

28 Jul '23

External Email - Use Caution Postdoc position in locus coeruleus connectomics of resilience at Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals at the post-doctoral level to work with Dr. Heidi Jacobs and Dr. Sepulcre. The Jacobs lab is part of the Gordon Center for Medical Imaging at MGH and focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 7T MRI, PET imaging, pupil measurements, physiological recording, blood-based markers, cognitive assessments and non-invasive vagus nerve stimulation. The Sepulcre lab is focused on connectomics, brain organization methods and the integration with genomics in neurodegenerative diseases. This project is focused on identifying locus coeruleus functional network properties conferring resilience against Alzheimer’s disease-cognitive decline in the face of pathology and identifying network properties indicating risk of Alzheimer’s disease. This project will require pulling and harmonizing large imaging datasets together to investigate locus coeruleus function across the disease continuum (e.g. ADNI, HABS, A4, 7T lifespan dataset,..). The Jacobs Lab consists of a multidisciplinary team of one instructor, five postdocs, three PhD-students, three clinical research coordinators and one project manager. The Sepulcre lab consists of one Assistant Professor, three postdocs and several students. Most of the work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of ongoing collaborations and be able to work in a stimulating and inspiring environment. The Department of Radiology at MGH is equipped with the first mobile PET/CT, the first brain PET/MRI, the first whole-body PET/MRI in the USA and several MRI scanners, including two 7T ultra-high-field scanner. It is equipped with a large-scale shared memory computing facility for parametric image analysis, tomographic reconstruction, Monte Carlo simulation, and other computationally intensive research applications. Our research group values open communication, motivation, optimism, mutual respect, teamwork, and innovative thinking. Dr. Jacobs and Dr. Sepulcre are highly committed to individualized mentoring to help trainees achieve the most out of their postdoctoral candidature and to move forward in their career. At a minimum, the training environment will include professional development, one-on-one meetings, group lab meetings, frequent seminars and journal clubs, opportunities to present their work at national and international scientific conferences (i.e. Human Amyloid Imaging, Alzheimer’s Association International Conference, OHBM), collaboration with partners within and outside MGH, and manuscript preparation for publication in high impact journals. In addition, both Dr. Jacobs and Dr. Sepulcre have a strong funding record and will strongly encourage and provide mentorship in grant applications. Requirements: Candidates should have a Ph.D. in Cognitive Neuroscience, Computational Neuroscience, Neuroimaging, Psychology (Biological) or related disciplines. Strong analytical, quantitative and programming skills and experience in fMRI are essential. Experience in connectomics or graph theory and physiological modeling would be beneficial. The candidate should be highly motivated, a strong communicator, possess internal drive to learn independently, but also be comfortable with working as part of a larger collaborative team. A real necessity is a passion for science, strong scientific writing and organizational skills, and a positive attitude. Experience in Alzheimer’s disease dementia or aging would be beneficial. [cid:image001.png@01D9C144.C546D1F0]MGH & HMS are equal-opportunity, affirmative action employers. Women and minority candidates are encouraged to apply. [cid:image002.png@01D9C144.C546D1F0]Apply: The successful candidate will have joint appointments at MGH and HMS. If interested, please send your CV, letter describing interests, background, major achievements, skills, goals and contact information for three professional references. Please send application materials to Dr. Heidi Jacobs, Associate Professor of Radiology, at hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu> Dr. Heidi Jacobs Associate Professor of Radiology Massachusetts General Hospital Harvard Medical School Department of Radiology Gordon Center for Medical Imaging 149 13th Street Charlestown, MA 02129 hjacobs(a)mgh.harvard.edu http://secure-web.cisco.com/14oqD7dprcCf49eSlNAiGL3dfmqKpOVamjNsxNS6scBIWTI…<http://secure-web.cisco.com/1l8SA-3A5ALVZmHlzYlFVe3deE2FBUxC5moRL1ibVx6-tRQ…> twitter: @HeidiJacobsLab Linkedin: https://secure-web.cisco.com/1bgtt7rjJgsPAg684dSO4VlzWiOCOo_NvGLrddliEe9jAE…

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Freesurfer