Freesurfer

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30061 discussions

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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SynthSeg QC - Reliable cut-off?
by AmirHussein Abdolalizadeh 15 Sep '23

15 Sep '23

External Email - Use Caution Hi, We're trying SynthSeg on data that has been improved using SynthSR. We are interested in the intracranial volume per se. I am curious how we can approach the QC metrics. Our first guess was to get an average for the QC metric of grey matter, white matter, and CSF (since they make ICV) and put an arbitrary cut-off to include reliable results. However, any comments are welcome. Best, Amir

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Re: [Freesurfer] registration error (reCAPTCHA not checked)
by fsbuild 14 Sep '23

14 Sep '23

External Email - Use Caution  The captcha authentication will not work if javascript is blocked from running in your browser.  Check that you browser preferences are not set to block/filter javascript in its preferences and/or by using some added browser extension.  I’m not aware that a firewall enabled on your machine or your ISP would otherwise block javascript from running. If your current browser does not work, you could do a clean install of some browser you do not currently have installed on your machine (w/o changing its default preference settings).   Choices for chrome based browsers you might not already have installed could be Vivaldi or Opera.  You could search for "download Vivaldi" or "download Opera" and go directly to that vendors web site and download the installer. - R. On Sep 6, 2023, at 09:21, lizhao_du(a)sjtu.edu.cn wrote:        External Email - Use Caution        Hi there,     I am Oscar. Recently I am using FreeSurfer for fMRI data analysis. A license is required yet I could not get the license.txt from my e-mail. After filling the form from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/registration.html, a registration error occured (see below).  Is there something wrong for my internet? Or what could I do to get the license?     A few words from you may help me a lot. Thanks in advance.<Catch7EDF(09-06-21-20-21).jpg>Best!Lizhao Du<InsertPic_799C(09-06-21-20-21).png> School of Biomedical Engineering, Shanghai Jiao Tong UniversityLizhao_Du@sjtu.edu.cn _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Password for FS Ubuntu virtual machine
by fsbuild 13 Sep '23

13 Sep '23

External Email - Use Caution The private email notice you received with the VM information explicitly stated NOT TO POST ANY PASSWORDS.   We will look to suspend the VM image and change the login credentials. - R. On Sep 11, 2023, at 17:23, Ynze Hokken <ylhokken(a)gmail.com> wrote:        External Email - Use Caution        Dear Sapere-Aude,The password is: Map.Brain321!Regards,Ynze HokkenOp ma 11 sep. 2023 om 23:21 schreef <sapere-aude@tuta.io>        External Email - Use Caution        Hi,I would like the password for the user "developer" in the FreeSurfer 7.2.0 Ubuntu virtual machine.Thanks!Regards,Sapere-aude_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Recon-all completed without error in 10 seconds
by Lauren Stephens 13 Sep '23

13 Sep '23

External Email - Use Caution Hi Freesurfers, I am attempting to run recon-all on a set of .nii.gz files. Each file is in our subject directory and has run through recon-all. Recon-all only takes 10 seconds to run and says it was completed without errors. When I go to the folder recon-all creates, the folders are empty. Here is the code we ran: recon-all -s 967 -i /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-00001-000208-01.nii.gz Here is the output message: Started at Wed Sep 13 10:52:44 PDT 2023 Ended at Wed Sep 13 10:52:54 PDT 2023 #@#%# recon-all-run-time-hours 0.003 recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023 done We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 7.3.2. I have attached the recon-all.log file and would appreciate any suggestions. We have previously run many successful recon-all's and have not encountered any issues. Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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