Freesurfer August 2020

freesurfer@nmr.mgh.harvard.edu

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Online Machine Learning School!
by Dwyer, Dominic Dr. 14 Aug '20

14 Aug '20

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Queries regarding installation of FreeSurfer software
by Dharmendra Jakhar 14 Aug '20

14 Aug '20

External Email - Use Caution I, Dharmendra Jakhar, a researcher working on brain mapping and an aspiring user of your software, is facing difficulties in installation of FreeSurfer software. Query 1- We have duly downloaded and installed the directory in the application folder, but we are getting a prompt in the terminal that 'No such file or directory is found'. We have attached the screenshot for your reference. Query 2- We are also not able to type License key password instead in its place we can see a 'key symbol'. We have also attached the screenshot for your reference.

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Contemplative Neuroscience Postdoctoral Position - Harvard Medical School/McLean Hospital
by Margiotta, Kathryn Nicole 13 Aug '20

13 Aug '20

[cid:image001.png@01D671A1.EF8F2F20] Postdoctoral Position in Contemplative Neuroscience at McLean Hospital/Harvard Medical School A postdoctoral position is available under the mentorship of Drs. Matthew D. Sacchet, David H. Rosmarin, and Diego A. Pizzagalli within the Laboratory for Affective and Translational Neuroscience (LATN) and Spirituality and Mental Health Program (SMHP) at McLean Hospital/Harvard Medical School. The LATN is part of the Center for Depression, Anxiety and Stress Research (CDASR; Directed by Dr. Pizzagalli; http://cdasr.mclean.harvard.edu/) a vibrant research center with over 40 scientists/staff/students that embraces a multi-disciplinary approach to improve our understanding of the psychological, environmental, and neurobiological factors associated with depression, anxiety, and related disorders across the lifespan The SMHP (Directed by Dr. Rosmarin; https://www.mcleanhospital.org/treatment/smhp) is a multifaceted initiative to meet the spiritual needs of McLean patients by providing spiritually-integrated care within multiple clinical programs throughout the hospital. In addition, the initiative provides chaplaincy services, develops new methods to incorporate faith into clinical treatment, conducts research on the relevance of spirituality to anxiety, mood, substance use, and other disorders, and trains and educates to raise greater awareness about spirituality and mental health. The candidate will be expected to lead and collaborate on projects that advance the neuroscience of prayer and meditation. The position will be primarily mentored by Dr. Sacchet, and secondarily by Drs. Rosmarin and Pizzagalli. Dr. Sacchet’s current research focuses on the neuroscience of advanced meditation and meditation training for depression (https://meditation.mclean.harvard.edu/) These studies employ a wide variety of approaches, including but not limited to high-density EEG, MEG, MRI (including functional, diffusion, and perfusion), computational modeling and machine learning, assays of hormonal/inflammatory markers, and wearables and experience sampling. Opportunities will be available to pursue independent research and interdisciplinary collaborations across Harvard Medical School. Depending on research focus, candidates will have access to research-dedicated human MRI scanners (3 T, 4 T, and 7 T), as well as two high-density EEG systems and a MEG system. Qualifications: A strong background in fast event-related and/or block design task-based functional MRI techniques is required. Expertise in contemplative neuroscience (e.g., prayer, meditation, and/or spirituality) is desired though not required. Additional experience with a second imaging modality and in clinical psychology and computational approaches (e.g., computational modeling, machine learning) will also be considered. To apply, send a CV, a cover letter describing research interests, as well as names and email addresses of three references to Matthew D. Sacchet (msacchet(a)mclean.harvard.edu<mailto:msacchet@mclean.harvard.edu>). Review of applications will begin immediately (expected start date: late 2020, although other timeframes may be possible). McLean Hospital, which is an affiliate of Harvard Medical School, is an Equal Opportunity Employer. As an equal opportunity employer, McLean seeks qualified candidates for all posted employment opportunities without regard to race, color, age, religion, gender, national origin, disability or veteran status. McLean particularly welcomes applications from minorities, women, and persons with disabilities. About the institution Since 1811, McLean Hospital has been a world leader in scientific investigations and treatments of mental illnesses as well as in training generations of scientists and clinicians. McLean Hospital maintains the largest program of research in neuroscience and psychiatry of any private psychiatric hospital in the United States. McLean Hospital has been ranked as America’s best freestanding psychiatric hospital for 18 consecutive years by U.S. News and World Report. U.S. News and World Report has consistently ranked Harvard Medical School as the best Research Medical School with the best Psychiatry Program. McLean Hospital is located in Belmont, Massachusetts, approximately 5 miles from Boston.

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mri_glmfit and R
by Eric Cunningham 13 Aug '20

13 Aug '20

External Email - Use Caution Hello Freesurfer Experts, I am trying to plot the ${meas} values at the maximum vertex in a significant cluster found by the group analysis pipeline (mri_glmfit). I created an .mgh file with mris_preproc, rh.cbd7.area.10.mgh. I read this file into matlab using MRIread. (mgh=MRIread(${path}/rh.cbd7.area.10.mgh);) After running mri_glmfit and mri_glmfit-sim, I found a significant cluster with maximum at vertex 53263. I read the values at this vertex using matlab again (values=mgh.vol(1,53263,1,:)). I then tried to duplicate the p value that mri_glmfit gave me at that vertex in R, and was unsuccessful (the p values did not match, and were actually quite different). I had assumed that mri_glmfit ran a glm at every vertex of the smoothed mgh file created by mris_preproc, and that the p values of that glm were assembled into sig.mgh. Was this assumption wrong? Thanks, -Eric

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Re: [Freesurfer] FreeSurfer 7.1.1 is released {Disarmed}
by fsbuild 13 Aug '20

13 Aug '20

External Email - Use Caution Hello Alex, Obtaining a license.txt file (and optionally using FREESURFER_HOME to point to its location) is listed here, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstalland here, https://surfer.nmr.mgh.harvard.edu/fswiki/rel6downloads - R. On Aug 13, 2020, at 16:42, Alexandru Hanganu <hanganu.alexandru(a)gmail.com> wrote:        External Email - Use Caution        Hi Freesurfer,can't find if this was reported.This refers to freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551.seems that in the new 7.1.1 version the required license file is located at FRESURFER_HOME/license.txt (instead of previous version .license)but this file is already present and includes the FreeSurfer license.workaround - rename the current FREESURFER_HOME/license.txt to e.g., license_freesurfer.txtcreate the FREESURFER_HOME/license.txt that includes the user's license details.Best,AlexLe lun. 27 juill. 2020, à 18 h 01, Douglas N. Greve <dgreve(a)mgh.harvard.edu> a écrit :FreeSurfer 7.1.1 is now available here https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloadsThis new version fixes bugs and adds some new features. Unless the new features are employed, it will give the same result as 7.1.0; consequently, results from subjects analyzed with 7.1.1 CAN be mixed with subjects analyzed with 7..1.0. Bug Fixes: Mac-related fixes:freeview/ PETSC error is now fixedfs_time now runs properlymri_cc does not crash when it can't find fornix (usually on mac)"preserve=timestamps" error fixed Memory leaks fixed (MRIScomputeMetricProperties). The excessive memory usage had caused some jobs to crash New Features: mris_volmask and mris_place_surface now have parallel implementations making recon-all faster tkregisterfv can now be run with --fstal (use this instead of tkregister2 to check the talairach registration) official FS docker container at https://hub.docker.com/r/freesurfer/freesurfer/____________________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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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FreeSurfer 7.1.1 is released
by Douglas N. Greve 13 Aug '20

13 Aug '20

FreeSurfer 7.1.1 is now available here https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads This new version fixes bugs and adds some new features. Unless the new features are employed, it will give the same result as 7.1.0; consequently, results from subjects analyzed with 7.1.1 CAN be mixed with subjects analyzed with 7.1.0. Bug Fixes: * Mac-related fixes: freeview/ PETSC error is now fixed fs_time now runs properly mri_cc does not crash when it can't find fornix (usually on mac) "preserve=timestamps" error fixed * Memory leaks fixed (MRIScomputeMetricProperties). The excessive memory usage had caused some jobs to crash New Features: * mris_volmask and mris_place_surface now have parallel implementations making recon-all faster * tkregisterfv can now be run with --fstal (use this instead of tkregister2 to check the talairach registration) * official FS docker container at https://hub.docker.com/r/freesurfer/freesurfer/

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Re: [Freesurfer] FreeSurfer 7.1.0 VirtualBox Installation password
by fsbuild 13 Aug '20

13 Aug '20

External Email - Use Caution I will send the password to your email shortly. - R. mudassar liaq August 13, 2020 at 10:19         External Email - Use Caution        Hi, I followed the given instructions on page (https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67) but could not find the README file to find the password to log in to the developer account. I've seen that other users in the archive received the password privately via email, can I  also request the password ?  Thanks in advance.  Liaq.  _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Available brain atlases in freesurfer in surface format!!
by Shreyas Indurkar 13 Aug '20

13 Aug '20

External Email - Use Caution Dear Freesurfer Experts, I came to know that freesurfer software contains atlas/atlases in surface format (.gii or similar). If yes, how is it possible to get access to these atlases? Thank you Sincerely, Shreyas Indurkar Max Planck Institute for Biological Cybernetics, Tuebingen, Germany.

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FreeSurfer 7.1.0 VirtualBox Installation password
by mudassar liaq 13 Aug '20

13 Aug '20

External Email - Use Caution Hi, I followed the given instructions on page ( https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67) but could not find the README file to find the password to log in to the developer account. I've seen that other users in the archive received the password privately via email, can I also request the password ? Thanks in advance. Liaq.

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Thalamic nuclei in FSL
by Erin Moe 13 Aug '20

13 Aug '20

External Email - Use Caution Hi Freesurfer experts, I ran segmentThalamicNuclei on my dataset and would like to use the segmentations on BOLD data in FSL using Featquery. I tried running vol2subfield but got an error: “set: Variable name must contain alphanumeric characters. I’ve tried a mired of other things to get the thalamic nuclei output into the mean_func.nii.gz space but haven’t had much success. What would you recommend I try? Terminal input for vol2subfield (note the dashes are double, my email client automatically changes them to single dashes): vol2subfield —i mean_func.nii.gz —reg $subject —$subject/mri/ThalamicNuclei.v12.T1.mgz —BOLD_thalamus.mgz Thanks! Erin

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Freesurfer August 2020