Freesurfer December 2022

freesurfer@nmr.mgh.harvard.edu

75 participants
92 discussions

Biannual Boston Freesurfer Workshops
by Salar Dini, Elaheh 09 Dec '22

09 Dec '22

External Email - Use Caution Hello dear freesurfer developers, I am leaving this message on the board to ask about the possibility of resuming the Boston Freesurfer course in the near future. The last update that I'm seeing on the Freesurfer official website pertains to the Spring 2020 course which is the one before the pandemic hit. Are you planning on resuming the biannual workshops anytime soon? Thanks and all the best, Ela

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A TRACULA Question
by Salar Dini, Elaheh 09 Dec '22

09 Dec '22

External Email - Use Caution Dear Anastasia, Thanks for your support in the past few months. I got an error message in -prep step: "Exception caught: itk::ExceptionObject (0x8a1e880) Location: "unknown" File: /home1/zs24/sandbox/build/ITKv5-install/include/ITK-5.0/itkSmoothingRecursiveGaussianImageFilter.hxx Line: 229 Description: itk::ERROR: SmoothingRecursiveGaussianImageFilter(0x8a1dd00): The number of pixels along dimension 2 is less than 4. This filter requires a minimum of four pixels along the dimension to be processed. ConvertTransformFile 3 /home1/es2263/TRACULA/subjects_dir/37/dmri/xfms/diff2syn0GenericAffine.mat /home1/es2263/TRACULA/subjects_dir/37/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras file /home1/es2263/TRACULA/subjects_dir/37/dmri/xfms/diff2syn0GenericAffine.mat does not exist . Linux ursapet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Oct 20 23:31:04 EDT 2022" I am attaching a log file too. Do you have a guess why this happened and how we can address it? One possibility is that we don't have all the dMRI sequence slices (like 300 out of 1600 are missing). Thanks for your time and help, Ela

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VM Password
by Mao, Andrew 08 Dec '22

08 Dec '22

External Email - Use Caution Hi, I'd like to request access to the Freesurfer VM. Thanks, Andrew Mao

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using FS7.2 tracula with FS6.0 outputs
by Alexopoulos, Dimitrios 08 Dec '22

08 Dec '22

External Email - Use Caution HI, we have run a cohort of 200 subjects through FS6.0 (including tracula) with good results. Is it possible to use the FS6.0 outputs (aparc+aseg, etc.) to run these data though only the updated tracula pipeline in 7.2? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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ma_ca_register is not called anymore in version 7.3.2
by Kilian M Pohl 08 Dec '22

08 Dec '22

External Email - Use Caution Hi , I have used the following call starting at Freesurfer 5.3 /usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon1 -noskullstrip -no-isrunning -s LAB_S01541_standard_20180307_4541_03072018 -rng-seed 1234 It is still working with Freesurfer 7.1.1 but we now tried updating to 7.3 and it is failing (on the same case). Looking at the recon-all.log it seem that ma_ca_register is not called anymore so that I get the following error message ERROR: cannot find or read transforms/talairach.m3z (see attached recon-all .log) Do I have to add flags ? I need to run with -noskullstrip Best, Kilian -- Kilian M. Pohl, Ph.D. Associate Professor Department of Psychiatry & Behavioral Sciences Stanford University 401 Quarry Road Stanford, CA 94305-5717 https://secure-web.cisco.com/18F69KCiyMWMSCouFYLrT3r9PgA1L7oUNzDa59-gQWUTsS…

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Regarding MRI Understanding.
by Rahul Sharma 07 Dec '22

07 Dec '22

External Email - Use Caution Hello everyone, I am very new to this neuroimaging and belongs to technical background. Could anyone provide me any source or material for understanding MRI scans and the neuroimaging tools such as Freesurfer or FSL. Eagerly waiting for your reply.

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Request for Assistance
by MANSON ERIC NAAB 07 Dec '22

07 Dec '22

External Email - Use Caution Dear Sir/Madam, I am Eric Naab, a Ph.D. student at the University of Ghana, and currently doing my research at the University of Ghana MRI Medical Center. The title of my research is "Optimization of Pulse Sequence Protocols for Magnetic Resonance Imaging of the Brain". I am working with a *1.5T MRI Philips scanner* and I intend to use the *FreeSufer software* for the first time*.* I would be very glad if you could provide me with the specific recommended protocol for imaging and any other assistance that could help me with my research. Thank you Counting on your usual cooperation.

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password request for file FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Daniele Ranieri 07 Dec '22

07 Dec '22

External Email - Use Caution Hello FreeSurfer, I downloaded VM from the official website: FS_7_2_0_ubuntu_18_04_06.ova.7z but I need the password to successfully open the compressed package. I hope that is the right place for this request. Thank you for your time.

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Password for Virtual Machine
by Sinani, Michelle 06 Dec '22

06 Dec '22

External Email - Use Caution Hi there! I recently tried downloading the freesurfer virtual machine but upon opening the download it asks for a password and I was wondering if that is something you can provide me with or where I can obtain it. Thank you very much! Best, Michelle Sinani, B.S. Data Manager Semel Institute of Neuroscience and Human Behavior UCLA Department of Psychiatry and Biobehavioral Sciences msinani(a)mednet.ucla.edu +1 (310)206-3512 x63512 ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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Neuroimaging Scientist Position - Massachusetts General Hospital, Department of Neurology
by Horn, Mitchell Jacob 06 Dec '22

06 Dec '22

Senior Research Technologist - (3220849) Background The Senior Research Technologist will perform duties in structural and functional magnetic resonance imaging at the Massachusetts General Hospital Stroke Research Center and the Athinoula A. Martinos Center for Biomedical Imaging. The research focus of this group is brain hemorrhage, which is a major cause of death and disability in the United States. We seek to understand what determines the risk of developing a brain hemorrhage as well as the consequences suffered after the hemorrhage occurs. Our lab has structural and functional MRI analysis pipelines that have resulted in multiple scientific articles published in first tier peer-reviewed Neurology journals. Responsibilities: The position will focus on the application of structural and functional image analysis algorithms in the study of brain aging and neurological diseases. The incumbent will work independently with minimal guidance of the Principal Investigator(s) and/or the Director of Clinical Research Operations and will collaborate with research fellows, clinical research coordinators and other research staff. Specific tasks may include: * Independently performs non-routine, highly specialized scanning sequences in accordance with study-specific MRI protocols * Develops research methodologies within parameters of experimental protocols and research objectives * Works with PI(s) in determining the most suitable design and methodology of research imaging protocols * Performs independent design and modification of protocols * Transfers, organizes, and summarizes acquired data * Prepares and presents research reports, manuscripts, posters or other documents for publication and/or presentation * Performs data analyses using advanced scientific, statistical and/or computational techniques * Responsible for troubleshooting problems and instructing others in highly specialized imaging and/or imaging data analysis techniques * Assists with other research/imaging-related tasks as needed Skills and competencies: * Excellent interpersonal, organizational and communication skills * Ability to work independently and as team member * Ability to make independent, effective decisions * High degree of computer literacy, including programming skills * Analytical skills and ability to resolve technical problems * Ability to effectively mentor and train junior research technicians * Demonstrated competence in research techniques and methodologies * Ability to identify problems and develop solutions * Bachelor's degree required, MA preferred Minimum Technical Standards: * Experience with MATLAB is required * Experience with Neuroimaging modalities (i.e., FreeSurfer, FSL, SPM) is strongly preferred * Experience with Linux/Unix and Bash Shell Scripting is strongly preferred * Proficiency in Microsoft Office is required * Experience with Statistical Software (i.e., SPSS, JMP etc.) is strongly preferred * Experience with Python is a plus Job description for Senior Research Technologist<https://partners.taleo.net/careersection/ghc/jobdetail.ftl?job=3220849&tz=G…> here, or can be found by searching job number 3220849 on the MGH Careers portal<https://www.massgeneral.org/careers>.

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Freesurfer December 2022