Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

Item shared with you: "Downloads.zip"
by Rebecca Elizabeth Cooper (via Google Drive) 26 Apr '22

26 Apr '22

External Email - Use Caution I've shared an item with you: Downloads.zip https://secure-web.cisco.com/1-oSwFXMVhHr2jh63UZQla8uWiUfbTDQCL-8u9LcpMsdv4… It's not an attachment -- it's stored online. To open this item, just click the link above.

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Request for 7Zip Archive passcode
by Logan Tate 26 Apr '22

26 Apr '22

External Email - Use Caution Hi, I made a prior request but believe the passcode was sent to someone who posted under my request, and not myself. I just need a passcode to archive the zip folder for file FS_7_2_0_Ubuntu_18_04_06.ova.7z Sorry for the spam! Thank you.

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Re: [Freesurfer] FreeSurfer 7Zip archive passcode
by fsbuild 26 Apr '22

26 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 25, 2022, at 04:59, Katharina Hense <Katharina.Hense(a)klinik.uni-regensburg.de> wrote:        External Email - Use Caution        Hello, I'm trying to expand the 7Zip archive for FreeSurfer on the VirtualBox. Can I get the passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z? Sincerely,Katharina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Request for Pass Code VP_7_2_0
by fsbuild 26 Apr '22

26 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 24, 2022, at 03:25, Kevin Wang <kwang001(a)yahoo.com> wrote:        External Email - Use Caution        Hello,I recently downloaded the archive for the file VP_7_2_0.  Could you please send the pass code required to expand the archive?  Thank you!Sincerely,Kevin_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Pass Code
by fsbuild 26 Apr '22

26 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 23, 2022, at 23:43, Activeingredient <activeingredient(a)proton.me> wrote:        External Email - Use Caution        Hi, can I get the password for FS_7_2_0_ubuntu_18_04_06.ova.7z?Thanks!_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Job posting: SRA at UCSD
by Wang, Xin 26 Apr '22

26 Apr '22

External Email - Use Caution Imaging Researcher University of California, San Diego. Apply in Institution’s website (https://secure-web.cisco.com/1SDJQkDq6j9d8jlPgTY38dMqz5jAkszVSyrb5fr9lxdmTS…) This position will work a hybrid schedule which includes a combination of working both onsite and remote. DESCRIPTION The research project will involve multiple neuroimaging studies examining biomarkers of brain aging and dementia. These studies will be partially conducted in collaboration with the UC San Diego Shiley-Marcos Alzheimer’s Disease Research Center. These studies will employ structural, diffusion and contrast MRI, amyloid and tau PET, neuropsychological testing, and blood and/or CSF biomarkers, among other tools, to better understand how brain microstructure, vascular integrity, and neuropathology, relate to disease risk and cognitive decline in Alzheimer’s disease or related dementias. Under the supervision of the project PIs (Drs. Reas and Banks), the incumbent will serve as a research project associate for multiple research protocols assessing neuroimaging biomarkers of dementia. Incumbent is responsible for organizing and managing brain imaging research data. Incumbent will manage Linux based workstations for post processing/data manipulation, and data analysis as well as create, maintain and update research databases. Provide support in project administration and publication preparation of imaging research. May provide assistance and have direct communication with subjects and families involved in research projects. MINIMUM QUALIFICATIONS · Bachelor's degree (psychology, neuroscience, biology, cognitive science, statistics, computer science or related field preferred) or equivalent work experience. · Proven knowledge of human subjects research policies and procedures. Knowledge of the human subject consent process, and federal government regulations pertaining to consenting of subjects. On-line training certificate (acquired on job). Knowledge of IRB, and sponsored research requirements. · Experience in a clinical trials research environment including basic understanding of persons with dementia, preferred experience with MRI in order to recruit, schedule, and test patients for clinical study subjects. · Thorough working knowledge of medical and scientific terminology. · Knowledge of statistical analysis of quantitative brain imaging data measures using SPSS, Matlab, and other statistical programs and prefer skills in coding. · Strong experienced with computers (Personal computer and Macintosh). Skill with personal computers, word processing, spreadsheet, e-mail software, databases, etc. Specifically Linux OS and the Microsoft office suite (excel, access, powerpoint, word, etc). · Proven ability to determine sources of clinical data, analyze the data and information obtained, in order to create documents and to propose solutions to issues and to help in developing standardized operational procedures. · Proven ability in researching clinical data in preparation for grant applications and technical manuals, staying abreast of new research developments. Ability to abstract information from protocol and investigator brochure, which requires summarizing large quantities of data. · Skill in assembling written narrative information using word processing software for documenting image analysis procedures and tracking data. · Excellent interpersonal skills with the ability to use tact and diplomacy with subjects (including patients with cognitive impairment), their families, faculty and institutional staff, as well as when representing the agency in the community. · Ability to collaborate and communicate effectively and diplomatically at all organizational levels, both verbally and in writing. Ability to work professionally and effectively with a diverse population, including the business community, academicians, staff and students. · Excellent record keeping, database management, detail oriented, logical, methodological approach to problem solving, strong process orientation, strong administrative and organizational skills with demonstrated ability to prioritize assignments, maintain workflow, and work productively in meeting critical deadlines and milestones. PREFERRED QUALIFICATIONS · Working knowledge of UCSD Human Research Protections Program policies and Procedures. SPECIAL CONDITIONS · Employment is subject to a criminal background check and pre-employment physical. If anyone is interested in this position, you could contact Dr. Reas (ereas(a)health.ucsd.edu) and Dr. Banks (sbanks(a)health.ucsd.edu<mailto:sbanks@health.ucsd.edu>) for further detail. Thanks.

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CC ROIs for FSL
by Hua, Jessica 26 Apr '22

26 Apr '22

External Email - Use Caution Hi FreeSurfer, The FreeSurfer atlas includes 5 corpus callosum regions. I am trying to create ROIs of those 5 regions and transfer them to FSL in .nii format to be used in DTI analyses. However, I have been unable to figure out how to put these ROIs in MNI152 space and transfer them to FSL. It was recommended that I run recon-all on the MNI template. Here is my code: recon-all -s John1 -i MNI152_T1_2mm_brain.nii -all -qcache -3T However when I try to run recon-all, I get the below message. Do you know why recon-all is not working (note: I tried this is 6.0 and 7.2)? And do you know how I can get FreeSurfer CC ROIS into MNI152 space and then convert them to FSL .nii files? #@# Curv .H and .K lh Mon Apr 25 18:54:14 PDT 2022 /Users/jessicahua/Box/John/John1/surf \n mris_curvature -w -seed 1234 lh.white.preaparc \n setting seed for random number generator to 1234 total integrated curvature = 16.045*4pi (201.629) --> -15 handles ICI = 107.1, FI = 655.1, variation=11743.051 writing Gaussian curvature to /Users/jessicahua/Box/John/John1/surf/lh.white.preaparc.K...done. writing mean curvature to /Users/jessicahua/Box/John/John1/surf/lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: lh.white.H: Function not implemented Darwin Jessicas-MacBook-Pro-2.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64 recon-all -s John1 exited with ERRORS at Mon Apr 25 18:54:17 PDT 2022 Thank you, Jessica

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Orthographic camera in FreeView
by Anderson M. Winkler 25 Apr '22

25 Apr '22

External Email - Use Caution Hi all, Is there a way to configure the camera in the 3D viewport in FreeView to use an orthographic projection instead of perspective (which currently is the default)? Orthographic used to be the default in tksurfer. A nice feature about it is that when we zoom, the effect is the same as scaling the projection (as opposed to introducing distortions). It makes a difference when we are collating screen captures for a figure, for example. I checked the help but don't seem to find any related option (in 7.2). Thanks! All the best, Anderson

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FreeSurfer 7Zip archive passcode
by Logan Tate 24 Apr '22

24 Apr '22

External Email - Use Caution Hello, I'm trying to expand the 7Z archive, and need a passcode.

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Request for Pass Code VP_7_2_0
by Kevin Wang 24 Apr '22

24 Apr '22

External Email - Use Caution Hello, I recently downloaded the archive for the file VP_7_2_0. Could you please send the pass code required to expand the archive? Thank you! Sincerely,Kevin

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