Freesurfer

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Convert Freesurfer segmentations to OBJ files
by Byripudi Naveen Kumar ed20d402 21 Sep '23

21 Sep '23

External Email - Use Caution Dear experts, I am trying to convert freesurfer segmentations to obj files for visualization in virtual reality. How to do this without losing any segmentation label names and colors. I tried to import the surfaces into 3d slicer but I could not do it. Also can you guide me on how to combine the tractography segments from tracula with the anatomical segmentations from recon-all? Thank you in advance Yours sincerely Naveen Kumar

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Training in Advanced Statistical Methods in Neuroimaging and Genetics, April 15 - 26, 2024
by ROBERT CARY WELSH 20 Sep '23

20 Sep '23

External Email - Use Caution Hi Folks, Our NIH-funded course, “Training in Advanced Statistical Methods in Neuroimaging and Genetics”, will be held in-person in Salt Lake City, UT, from April 15 - 26, 2024. This is a course geared to advanced undergraduate students graduate students, postdocs, and junior faculty. Topics include (see website for more details): Bayesian methods of functional connectivity and activation, longitudinal modeling, network neuroscience, polygenic risk scores, multimodal modeling and predictive modeling. The course is a mix of lectures and hands-on computer labs. Our main lecturers include: Martin Lindquist, Johns Hopkins University Mandy Mejia, Indiana University Rick Betzel, Indiana University Anna Docherty, University of Utah To read more about the course and to apply please see: neurostatsbootcamp.org<http://secure-web.cisco.com/1WGCNO64hrsDRKsP26U8raRZJtaEs4uG-nIYndj55ZcaHIY…> The application (which is multi-part, so please read the detailed instructions) deadline is November 1, 2023. We also offer a limited number of need-based tuition-reduction awards. This is a not-for-profit course and faculty are supported by NIH R25NS117281. Prior testimonials, “This course changed my life”, “I truly learned a lot!”, “This was an excellently planned course.” For more information email us at neurostats(a)g.ucla.edu Best, Robert and Anna ----------- Robert Welsh Professor-in-Residence UCLA Anna Docherty Associate Professor University of Utah

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Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan
by fsbuild 19 Sep '23

19 Sep '23

External Email - Use Caution Hello Ken, The output from your linux shell limits in the log show the following, cputime      unlimitedfilesize     unlimiteddatasize     unlimitedstacksize    8192 kbytescoredumpsize 0 kbytesmemoryuse    unlimitedvmemoryuse   unlimiteddescriptors  1024 memorylocked 64 kbytesmaxproc      7823 maxlocks     unlimitedmaxsignal    7823 maxmessage   819200 maxnice      0 maxrtprio    0 maxrttime    unlimited I would set at least coredumpsize to something non-zero so you can at least get a core file saved that could be looked at.   By default the limits on my Ubuntu 22 system are: $ ulimit -areal-time non-blocking time  (microseconds, -R) unlimitedcore file size              (blocks, -c) unlimiteddata seg size               (kbytes, -d) unlimitedscheduling priority                 (-e) 0file size                   (blocks, -f) unlimitedpending signals                     (-i) 378881max locked memory           (kbytes, -l) 64max memory size             (kbytes, -m) unlimitedopen files                          (-n) 1048576pipe size                (512 bytes, -p) 8POSIX message queues         (bytes, -q) 819200real-time priority                  (-r) 0stack size                  (kbytes, -s) 8192cpu time                   (seconds, -t) unlimitedmax user processes                  (-u) unlimitedvirtual memory              (kbytes, -v) unlimitedfile locks                          (-x) unlimited You can try setting the core file size to unlimited with, $ ulimit -c unlimited... then check the value was changed to something > 0 ...$ ulimit -a You could increase memory size (and as many shell limits as possible) to unlimited to get the max size allowed by the system in the script you use to run recon-all, and then try running recon-all  again to see if you can retrieve a core dump file. - R. On Sep 16, 2023, at 09:55, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:        External Email - Use Caution        OK, I've attached the log file. ------- Original Message -------On Friday, September 15th, 2023 at 2:59 PM, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution         It might help if you could send along the crash report as an attachment..-R.On Sep 15, 2023, at 14:36, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:        External Email - Use Caution        Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE scan and got the "mri_convert: segmentation fault (core dumped)" error again. Any clarity on this issue would be appreciated. Thanks,K------- Original Message -------On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:Howdy yall,I ran a subject through synthsr (freesurfer 7.4) and am trying to run the output through the freesurfer 5.1 pipeline (the rest of my dataset was processed with 5.1). I am getting the error "Segmentation fault (core dumped)" during the mri_convert step. Any suggestions? Thanks,Ken_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] freeview upgrade isn’t working/library issue
by fsbuild 19 Sep '23

19 Sep '23

External Email - Use Caution  I don't think we can guarantee upgrading freeview will work with the existing libraries in a sufficiently old freeview distribution.  I’m not sure what version of Ubuntu is running from the kernel listed below, but you could create a backup of your existing freesurfer tree (if you need to keep it), and then run the .deb freesurfer 7.4.1 installer matching your system (Ubuntu 18, 20, 22) which you can download from,  https://secure-web.cisco.com/1W5Z7do8RHfQJIQIHZ9EbWhe5GYVhLQ8shO8lqEwhsAE6g… - R. On Sep 19, 2023, at 15:33, Hoptman, Matthew (NKI) <Matthew.Hoptman(a)nki.rfmh.org> wrote:        External Email - Use Caution        TO: freesurfer@nmr.mgh.harvard.eduFROM: matthew.hoptman@nki.rfmh.orgSUBJECT: freeview upgrade isn’t working/library issue Hello FreeSurfer Developers, I followed the instructions here to upgrade freeview:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeviewI am now getting the error: freeview: error while loading shared libraries: libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file or directory I saw that it was recommended to install the package libvtk7.1, but that isn’t working:E: Unable to locate package libvtk7.1E: Couldn't find any package by glob 'libvtk7.1' Any help is appreciated. I am using:5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 x86_64 x86_64 GNU/LinuxThanks, Matt  IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail.PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Recall: freeview upgrade isn’t working/library issue
by Hoptman, Matthew (NKI) 19 Sep '23

19 Sep '23

External Email - Use Caution Hoptman, Matthew (NKI) would like to recall the message, "freeview upgrade isn’t working/library issue". ________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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freeview upgrade isn’t working/library issue
by Hoptman, Matthew (NKI) 19 Sep '23

19 Sep '23

External Email - Use Caution TO: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> FROM: matthew.hoptman(a)nki.rfmh.org SUBJECT: freeview upgrade isn’t working/library issue Hello FreeSurfer Developers, I followed the instructions here to upgrade freeview: https://secure-web.cisco.com/1Fr1m43dMDo6PfZjwvbGiKtV6gtUUqAq08NIpRJf8nkhbp… I am now getting the error: freeview: error while loading shared libraries: libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file or directory I saw that it was recommended to install the package libvtk7.1, but that isn’t working: E: Unable to locate package libvtk7.1 E: Couldn't find any package by glob 'libvtk7.1' Any help is appreciated. I am using: 5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Thanks, Matt IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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TRACULA cluster visualization - mri_glmfit-sim issue?
by Goeckner, Bryna 18 Sep '23

18 Sep '23

External Email - Use Caution Hi Freesurfer Developers, I am having an issue similar to two posted earlier this year with the visualization of significant clusters from tracula not seeming to match the data. (link to first posting here: https://secure-web.cisco.com/1YIyp3Yo44Yjw3sCRGiQdzImJfJAVEC8lOoyUpu2pWJi9R…) Specifically, when mri_glmfit is first run, the data and initial visualization of the significant voxels along the lh cingulum bundle (dorsal) make it appear that the area with the most significant effect is in the anterior part of the tract (see sig_overlay.png). When mri_glmfit-sim is run, the text file of the significance values masked by clusters that survive correction also makes it appear that the significant effects would be in the anterior portion of the tract because they are at the top of the text file (see perm.th13.abs.sig.masked.txt), and earlier data, in agreement with information on the tracula page, is given anteriror to posterior along this tract. This matched what I would expect given the data before clusterwise correction. However, the visualization of the masked significance values seems to show only posterior areas with effects (see sigmasked_overlay.png) I am wondering if there is something in the mri_glmfit-sim process that woucl be causing this apparent flip in the visualization or if there is something I need to be doing differently. Please let me know if you need any additional information and thanks in advance for your help! My code: mri_glmfit --y ${STATDIR}/${TRACT}.avg16_syn_bbr.${MET}.nii.gz --fsgd ${STATDIR}/${STUDY}/inputs/${FSGD}.fsgd doss --C ${STATDIR}/${STUDY}/inputs/${C}.mtx --o ${STATDIR}/${STUDY}/${C}/${TRACT}.${MET}.glmdir --save-eres mri_glmfit-sim --glmdir ${STATDIR}/${STUDY}/${C}/${TRACT}.${MET}.glmdir --cwp 0.05 --perm 1000 1.3 abs To create visualizations: dmri_trk2trk --in /opt/freesurfer/trctrain/hcp/syn/${TRACT}.display.trk --out ${STATDIR}/${STUDY}/${C}/${ResFol}/${TRACT}.${MET}.maskedoverlay.trk --over ${STATDIR}/${STUDY}/${C}/${TRACT}.${MET}.glmdir/${C}/perm.th13.abs.sig.masked.mgh To create text file from mri_glmfit-sim makes output: mri_convert --ascii perm.th13.abs.sig.masked.mgh perm.th13.abs.sig.masked.txt Bryna Goeckner (she/her) Graduate Student Meier Lab<https://secure-web.cisco.com/1L0DdRAsArvZ7gyFkPi0YnO8htwQ03fLvWrtjVgm-rwoJR…> Medical College of Wisconsin Neuroscience Doctoral Program

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Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan
by fsbuild 16 Sep '23

16 Sep '23

External Email - Use Caution  It might help if you could send along the crash report as an attachment. -R. On Sep 15, 2023, at 14:36, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:        External Email - Use Caution        Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE scan and got the "mri_convert: segmentation fault (core dumped)" error again. Any clarity on this issue would be appreciated. Thanks,K------- Original Message -------On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:Howdy yall,I ran a subject through synthsr (freesurfer 7.4) and am trying to run the output through the freesurfer 5.1 pipeline (the rest of my dataset was processed with 5.1). I am getting the error "Segmentation fault (core dumped)" during the mri_convert step. Any suggestions? Thanks,Ken_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_convert: Segmentation fault (core dumped) synthsr scan
by KennethSPrice 15 Sep '23

15 Sep '23

External Email - Use Caution Howdy yall, I ran a subject through synthsr (freesurfer 7.4) and am trying to run the output through the freesurfer 5.1 pipeline (the rest of my dataset was processed with 5.1). I am getting the error "Segmentation fault (core dumped)" during the mri_convert step. Any suggestions? Thanks, Ken

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Postdoctoral Position in Advanced Clinical Neuroimaging of Aging, Dementia, TBI, and PTSD in Veterans
by Boston NeRVe 15 Sep '23

15 Sep '23

External Email - Use Caution *Postdoctoral Position in Advanced Clinical Neuroimaging of Aging, Dementia, TBI, and PTSD in Veterans* *Applicants must be US Citizens* *Location:* VA Boston Healthcare System, Boston, MA *Affiliated Laboratories and Investigators: * Translational Research Center for TBI and Stress Disorders (TRACTS) National Center for Post Traumatic Stress Disorder (NCPTSD) Neuroimaging Research for Veterans Center (NeRVe) Catherine Fortier, PhD William Milberg, PhD Michael Esterman, PhD David Salat, PhD *Position Type:* Full-Time, 2-year contract with potential for renewal. --- *VA Boston:* VA Boston Healthcare System is a premier research institution at the intersection of neuroimaging, cognitive neuroscience, and clinical research in Veterans. Located in the dynamic and eclectic Jamaica Plain neighborhood of Boston, we offer state-of-the-art neuroimaging facilities, dedicated research teams, and a vibrant, interdisciplinary research environment. We are committed to understanding the neurological intricacies of aging, Alzheimer's, dementia, combat exposure, traumatic brain injuries, PTSD, and more. --- *Role Description:* Seeking a highly motivated and skilled Postdoctoral Fellow to lead groundbreaking research in advanced clinical neuroimaging. This pivotal role will integrate methodologies from computer vision, machine learning, and neuroimaging to investigate the neural underpinnings of aging, Alzheimer's, dementia, and the unique challenges faced by Veterans. --- *Key Responsibilities:* 1. Conduct advanced neuroimaging data acquisition using fMRI, DTI, and other modalities. 2. Process and analyze large datasets leveraging state-of-the-art computer vision and machine learning techniques. 3. Collaborate closely with computer scientists, neuroscientists, and clinicians to design and implement innovative experiments. 4. Publish research findings in high-impact journals and present at international conferences. 5. Mentor junior researchers, graduate students, and interns. --- *Qualifications:* 1. Ph.D. in Neuroscience, Computer Science, Cognitive Neuroscience, or related fields. 2. Proficient in neuroimaging tools (e.g., FSL, SPM, AFNI, Freesurfer) and programming languages (e.g., Python, MATLAB). 3. Demonstrated expertise in computer vision and/or machine learning applications. 4. Strong publication record in relevant domains. 5. Excellent interpersonal and collaborative skills. --- *What We Offer:* 1. Competitive salary and benefits package. 2. Access to state-of-the-art neuroimaging facilities and computational resources. 3. Collaborative environment with world-renowned experts. 4. Strong focus on professional growth and networking. --- *How to Apply:* Interested candidates should send a CV, a cover letter detailing relevant experience, and the names and contact details of three references to Dylan Katz (Dylan.Katz(a)va.gov) --- Closing Date: 12/10/2023 --- VA Boston Healthcare System is an equal opportunity employer. We encourage applications from candidates of all backgrounds and experiences.

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