Freesurfer

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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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TRACULA tutorial and processing questions
by Tran, Diana 05 Dec '22

05 Dec '22

Dear FreeSurfer TRACULA experts, I am new to FreeSurfer and using TRACULA to process DTI data. From the mail-archive, I understand TRACULA mainly needs the aparc+aseg output from recon_all in order to run. Using the recon_all output information, I was able to complete the 3 steps in TRACULA, but only after switching from the 7.1.1 version to the 6.0.5.1 version of FreeSurfer. I have the following questions about TRACULA: 1. Some of the tutorial files that are needed to run the TRACULA tutorial are not there upon downloading or do not match the tutorial instructions. Is there an updated version of the tutorial instructions that match the current files? 2. Do you have insight as to why TRACULA -prep exits with ERRORS when it's run with version 7.1.1 of FreeSurfer, but exits without errors when it's run with version 6.0.5.1? Reviewing the scripts, it seems the most notable difference are the values for i_ras, j_ras, and k_ras. Version 6.0.5.1 gives varying numbers, while version 7.1.1 gives values of -1, 0, or 1. 3. I came across the webpage introducing version 7.2 with substantial updates for TRACULA after having run my dataset with version 6.0 (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) It states, "Unless the new features are employed, recon-all will give the same exact result as 7.1.1 and 7.1.0." Is this also true for TRACULA? Would you advise rerunning my dataset with version 7.2 of TRACULA (or even 7.3, but the recent release notes for this version didn't mention TRACULA changes)? 4. Is there another location to find the dwi_motion_byvol.txt output file? Currently the instructions say it should be located in the /subject#/dmri folder but only the dwi_motion.txt can be found there (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs) 5. For some subjects with visible motion distortions in manual quality check, I ran TRACULA as a second QC measure. However, they are still given a score of 0 and 1 for percent bad slices and average dropout score, respectively, according to the dwi_motion.txt. In fact, for all the subjects I ran, they all received those scores with the exception of one subject, who actually had minimal motion artifacts in manual QC. I'm not sure how to interpret this and was wondering if you could please advise. 6. While combing through the mail-archive to better understand how to use TRACULA, I noticed dt_recon being mentioned with TRACULA processing. Is this a step that needs to be completed before running TRACULA? Or is it part of an older version of processing that is already built into the updated versions 6.0+ of TRACULA? Thank you in advance for your time! Warm regards, Diana

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SynthSR and Apple M1 Incompatability
by Sorby-Adams, Annabel 05 Dec '22

05 Dec '22

Dear FreeSurfers, I have been trying to get SynthSR up and running and have come to the realisation there is a conflict with the current tools and the new apple chips (macOS Monterey, Apple M1 chip, 16GB). I have tried the workaround via this thread on the mailing list to no avail (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg73091.html) I then tried to install homebrew, conda, and run a virtual environment which allowed me to download tensorflow. The steps I followed with comments are attached. However, now there is an issue when calling mri_synth as follows: File "/Applications/freesurfer/dev/python/scripts/mri_synthsr", line 18, in <module> import tensorflow as tf ModuleNotFoundError: No module named 'tensorflow' I am not sure if there is a disconnect in where I have installed tensorflow such that mri_synthsr is unable to locate it. If anyone has found a workaround for this they would be willing to share it would be greatly appreciated! Thanks, Annabel Annabel Sorby-Adams, PhD Fulbright Postdoctoral Research Fellow Department of Neurology Massachusetts General Hospital Lunder 6 55 Fruit Street, Boston MA https://www.massgeneral.org/ Harvard Medical School https://hms.harvard.edu/ E asorby-adams(a)mgh.harvard.edu T +1 617 251 6465

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