Freesurfer

freesurfer@nmr.mgh.harvard.edu

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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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Pass Code
by Activeingredient 23 Apr '22

23 Apr '22

External Email - Use Caution Hi, can I get the password for FS_7_2_0_ubuntu_18_04_06.ova.7z? Thanks!

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pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Peng, Shichun 23 Apr '22

23 Apr '22

External Email - Use Caution Could you please send me the pass code to unzip the file? Thanks, Shichun The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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ERROR: Talairach failed!
by Fritze, Stefan 23 Apr '22

23 Apr '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute recon-all -all -subjid XXX -qcache -3T, which works fine with most of my study participants, but for some of them I receive Talairach error (s. error message below): I've searched the list and similar errors have been reported and there is a webpage dealing with this type of error (https://secure-web.cisco.com/1RvZhQl7xG9ZOQtDHxIejsIaxH-Szi0GVQwXNg3elCyaJx…) Yet, tkregisterfv produces also an error, even when I do not set the --surf orig flag (the surf folder of these participants is empty). Running the mritotal utility from the MNI toolset produces the same error. In one participant, the problem was solved when I converted the .nifti file to .mgz and started recon-all from there. But this did not help with the other participants. Including the -notal-check flag allows recon-all to complete, yet I do not know whether the results are trustworthy. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 2) Platform: 54G7T63 Kernel: 5.0.0-32-generic x86_64 bits: 64 compiler: gcc v: 7.4.0 Desktop: MATE 1.22.2 wm: marco dm: LightDM Distro: Linux Mint 19.3 Tricia base: Ubuntu 18.04 bionic 3) recon-all.log: see attached Best wishes, Stefan #@# Talairach Failure Detection Fr 11. Mär 18:44:03 CET 2022 talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0321, pval=0.0034 < threshold=0.0050) Command exited with non-zero status 1 @#@FSTIME 2022:03:11:18:44:03 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100% M 6312 F 0 R 247 W 0 c 0 w 1 I 0 O 0 L 83 1 60 @#@FSLOADPOST 2022:03:11:18:44:03 talairach_afd N 4 83 1 60 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://secure-web.cisco.com/13BLRYoRPHBMar5-JIvMd4hV-rXEV8EfKJNo4h7T066Q_Rp… ERROR: Talairach failed!

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mri_segment_hypothalamic_subunits error
by Chen ZY 22 Apr '22

22 Apr '22

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to use the mri_segment_hypothalamic_subunits tool on subjects that have been analyzed with recon-all as described on the wiki page (https://secure-web.cisco.com/1A9dGY6OywLZ30vDfBWiSZqvoBp25mO3nhNd6jDNfiis58…) but I received the following error when I run the mri_segment_hypothalamic_subunits command (mri_segment_hypothalamic_subunits --s): (tensorflow) brain@neurodebian:/usr/local/apps/freesurfer/subjects$ mri_segment_hypothalamic_subunits --s bert using 1 thread processing 1/1 *** Error in `/usr/local/apps/freesurfer/python/bin/python3': munmap_chunk(): invalid pointer: 0x00007fa1707b3400 *** Aborted I would be appreciated if you can help me solve this problem. Thank you very much! Regrads, 发送自 Windows 10 版邮件<https://secure-web.cisco.com/1CLa9ah2pQJGRCoKdiDPebrBBXr4zULmqXF8tkJypVTxDs…>应用

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Re: [Freesurfer] License for 5.X versions of FreeSurfer
by fsbuild 21 Apr '22

21 Apr '22

External Email - Use Caution Responding to you off the list. - R. On Apr 21, 2022, at 15:08, Paul Wighton <paul(a)corticometrics.com> wrote:        External Email - Use Caution        Hi Jacob,Can you provide more details on how FreeSurfer was installed, how you are using the license key and the errors you are receiving?I just created a docker container with FreeSurfer v5.3.0-HCP (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1J8ksi9SDc5fMzjSvEALj9L1iRGatYnyqft703…) and tried my license file and things work fine.The container is at pwighton/freesurfer:5.3.0-HCP if you would like to try it yourself.You can run `docker run -it --rm pwighton/freesurfer:5.3.0-HCP` to get an interactive shell inside this container.Once inside the container, running this test command:```mri_convert /opt/freesurfer-5.3.0-HCP/subjects/sample-001.mgz /tmp/sample-001.nii.gz```Does indeed give me a license error```--------------------------------------------------------------------------ERROR: FreeSurfer license file /opt/freesurfer-5.3.0-HCP/license.txt not found.  If you are outside the NMR-Martinos Center,  go to MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1ky0Zkng4jenq5LESezo6mVh5Nj2QyMfpmBaZ_E… get a valid license file (it's free).  If you are inside the NMR-Martinos Center,  make sure to source the standard environment.--------------------------------------------------------------------------```However after copying my license file to `$FREESURFER_HOME/license.txt` the same command works fine.-PaulOn Thu, Apr 21, 2022 at 3:42 AM Jacob Breiting Sönnichsen <jbs(a)brainreader.net> wrote:        External Email - Use Caution        Hi all, Are there really no one out there, who knows, how we can get a FreeSurfer 5.1 and 5.3 running?How do we obtain/create a license for these versions? Kind regards / Cordialement / Med venlig hilsen Jacob From: Jacob Breiting Sönnichsen Sent: Friday, 15 April 2022 10.03To: freesurfer@nmr.mgh.harvard.eduSubject: License for 5.X versions of FreeSurfer How do I obtain a license to run old versions of FreeSurfer?I need to replicate some research done with an old 5.1 and 5.3 version of FreeSurfer and using a current license does not seem to work?Is it possible to convert the new license to the old license somehow? Kind regardsJacob_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16KPMReTC7GusLUXzm69NkGs_u2h1TtCJQJxIH… information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/193_FpqrceBj1EcwaA5EiWd5AF7LL6sUh3tGks… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1qAm2kFjt5n_Pli8LvxfUKUqwOvUgLPLr8BxRp…; .Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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