Freesurfer July 2023

freesurfer@nmr.mgh.harvard.edu

93 participants
130 discussions

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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Re: [Freesurfer] freeview error....
by fsbuild 27 Jul '23

27 Jul '23

External Email - Use Caution  Hello Gonzalo, If you have not already done so, then I suggest installing the  .deb installer package for 7.3.2 from, surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer_ubuntu18-7.… - by cd’ing to where you downloaded the above file to on your machine and then running, $ sudo apt install ./freesurfer_ubuntu18-7.3.2_amd64.deb Then test the environment with, $ export FREESURFER_HOME=/usr/local/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh $ which freeview$ /usr/local/freesurfer/7.3.2/bin/freeview … check freeview comes up with an empty window … $ freeview … then quit and try viewing an example volume … $ freeview  $FREESURFER_HOME/subjects/bert/mri/brain.mgz - R. On Jul 27, 2023, at 10:15, Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:        External Email - Use Caution        Hi:  I have Ubuntu 18.04.4 LTS and freesurfer release freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275. When I run freeview, I got the error:"This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb."  How can I correct it?  Sincerely,Gonzalo Rojas Costa_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freeview error....
by Gonzalo Rojas Costa 27 Jul '23

27 Jul '23

External Email - Use Caution Hi: I have Ubuntu 18.04.4 LTS and freesurfer release freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275. When I run freeview, I got the error: "This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb." How can I correct it? Sincerely, Gonzalo Rojas Costa

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Tracula -bedp and -prep exited with errors
by Ramtilak Gattu 26 Jul '23

26 Jul '23

External Email - Use Caution Hello, The following command trac-all -c dmrirc.example -bedp always exits with the following error. { WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 -model 1 /home/developer/Desktop/DATA_VB/Data/TRACULA/trc/Sub_01/dmri /usr/local/freesurfer/7.4.1/freesurfer/bin/bedpostx_mgh: 128: /usr/local/freesurfer/7.4.1/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected } The processing doesn't even get started. It exits immediately I tried freesurfer 7.2 and 7.4.1 versions on virtual box thinking there might be some problem with the bedpostx_mgh source code. But it does the same with both the versions. Trac-all with -prep argument runs for a while and exited with { Pre-sorted training .trk file detected INFO: Rejected 114 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction INFO: Have 19886 total streamlines (min/mean/max length: 60/88/115) Processing pathway 29 of 42... INFO: Have 19886 non-truncated streamlines (min/mean/max length: 60/88/115) Computing path histograms INFO: Total streamline volume is 25477 voxels Finding outlier streamlines Updating streamline distance ranking INFO: Split streamlines into 25 segments Computing prior on underlying anatomy (all streamlines) Killed Linux developer-VirtualBox 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Jul 26 18:08:00 EDT 2023 } -Prep getting killed because of insufficient memory?? Can someone please help. Thanks Regards Tilak

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Pass code
by Jonathan Hamilton 26 Jul '23

26 Jul '23

External Email - Use Caution Hi there, I am trying to download and run the virtual machine as described on this page: VM_67 - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1qcup5hX2WfiN6c5wRiqamyJLkxEnliLGIxAi4ShSWJsP5…> It is asking for a pass code and the instructions say to email this list for one, could I please be sent one? Thank you, Jonathan

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Freesurfer July 2023