Freesurfer September 2021

freesurfer@nmr.mgh.harvard.edu

76 participants
107 discussions

Re: [Freesurfer] Requirement for Ubuntu_710_clone-disk1 'developer' password
by fsbuild 09 Sep '21

09 Sep '21

External Email - Use Caution Sending the info to your personal email shortly. - R. On Sep 9, 2021, at 11:29, Huang Chen-Wei <dreamweaver0314(a)gmail.com> wrote:        External Email - Use Caution        Hello developer,After booting up Freesurfer v7.1.0 by following the installation guide, a developer account login is prompted, but I could not find any information in the documentation. Would you please help me to solve this problem? Thanks!Daniel不含病毒。MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1a5mAZeJ8f_3oCOZ66ajYvAt1Yk3BfD6CG2gSy5… mailing listFreesurfer@nmr.mgh.harvard..eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Segmentation error
by halil ibrahim AKÇAY 09 Sep '21

09 Sep '21

External Email - Use Caution Hi again, When I check my mri images for segmentation errorin freesurfer, I can see dimple in 3D view of freesurfer and I would like to fix it. But I cannot find any problem in 2D view. Should I accept this dimple as a problem or ignore it? If this is a problem, how can I fix it? I am sending a screenshoot of dimple in freesurfer. Thanx Halil

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Requirement for Ubuntu_710_clone-disk1 'developer' password
by Huang Chen-Wei 09 Sep '21

09 Sep '21

External Email - Use Caution Hello developer, After booting up Freesurfer v7.1.0 by following the installation guide, a developer account login is prompted, but I could not find any information in the documentation. Would you please help me to solve this problem? Thanks! Daniel <https://secure-web.cisco.com/1bAIZSRX3DckIvnPAzM6SBsvre4uB4VkE8PYyTURP3_ksX…> 不含病毒。http://secure-web.cisco.com/1r1Zmvc2wTb6BtilVxZpgq0UZ9z4HHUhAbO1sizQig… <https://secure-web.cisco.com/1bAIZSRX3DckIvnPAzM6SBsvre4uB4VkE8PYyTURP3_ksX…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Password Ubuntu VM
by Daniel Chiaretti 09 Sep '21

09 Sep '21

External Email - Use Caution Dear Freesurfers, I am trying to set up the virtual box freesurfer. However, after starting up the virtual machine it is asking for a password for the 'developer' user. Which password should I use? Thanks in advance, Daniel

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recon-all terminated by signal 11 at various points (eg. mri_normalize, mris_place_surface)
by Falko Mecklenbrauck 08 Sep '21

08 Sep '21

External Email - Use Caution Dear Freesurfer Developers, I'm attempting to compute the complete reconstruction of the structural data of my participants. Therfore I'm using the following commands through a shell-script. /export FREESURFER_HOME=/usr/local/freesurfer// //source $FREESURFER_HOME/SetUpFreeSurfer.sh// //export FS_LICENSE= <path to license.txt>// //SUBJECTS_DIR= <path to folder with nifti of Subject>// / / inputFn1= <path to nifti-file>// // outputDir= < path to output directory of participant>// // mkdir $outputDir// // mkdir $outputDir/mri// // mkdir $outputDir/mri/orig// // outputFn1=$outputDir/mri/orig/001.mgz// // mri_convert $inputFn1 $outputFn1// //// // recon-all -s "<subject ID>" -autorecon-all/ After trying the command a couple of times on diffrent profiles, I'm always greeted with the message "Command terminated by signal 11" without having a real ERROR message. I attached two recon-all.log files, where the process stopped on mri_normalize and mris_place_surface respectively. 1) Freesurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu 20.04.3 LTS (Codename: focal) 3) uname -a: Linux THALAMUS 5.4.0-81-generic #91-Ubuntu SMP Thu Jul 15 19:09:17 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) both recon-all.log attached (signal_11_mri_normalize_recon-all.log and signal_11_mris_place_surface_recon-all.log) Unfortunately the nifiti-File is to big to be attached. If you need it, what would be the best way to share it with you. Thank you very much in advance! Best wishes, Falko

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preproc-sess output
by Alice Giubergia 08 Sep '21

08 Sep '21

External Email - Use Caution Dear Freesurfer's experts, I got a beginner questiom 'cause I am new in Freesurfer. I ran preproc-sess on my functional data: preproc-sess -s sessionid -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run and got fmcpr.up.sm5.fsaverage.lh.nii.gz for data sampled to the left hemisphere of fsaverage. I was trying to visualize these data through freeview -v since I succesfully opened the orginal data f.nii, but got nothing. What's my error? any suggestion?

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Recon-all error: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage
by Szulia Agata 07 Sep '21

07 Sep '21

External Email - Use Caution Hi, I have a problem with running recon-all on some subjects. Mostly, it does exit without errors, however sometimes it exits with "ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version”. I have only one version of fs installed - 7.2.0. Does anyone know why does it happen and how to proceed with recon-all in such cases? I attach recon-all log files. Thank you very much for your help, Agata Klauzula poufności. Ta wiadomość pocztowa i wszelkie załączone do niej pliki są poufne i podlegają ochronie prawnej. Jeśli nie jesteś jej prawidłowym adresatem, jakiekolwiek wykorzystanie w tym zapoznanie się z treścią przesłanych informacji, jej ujawnienie, reprodukcja, dystrybucja lub inne rozpowszechnienie, są ściśle zabronione. Jeśli otrzymał/a Pan/i niniejszy przekaz wskutek błędu, proszę o niezwłocznie powiadomienie nadawcy i usunięcie otrzymanych informacji. Kontakt: Uniwersytet Medyczny w Łodzi, 90–419 Łódź, Al. Kościuszki 4, Rektorat – Centrala, Tel. 42 272 59 66 umed.lodz.pl Confidentiality Notice - This e-mail is confidential, may be legally privileged. If you are not the intended recipient, you may not use, disclosure, distribute, copy, print or rely on this e-mail. If you received this e-mail in error, please notify the sender and delete the material from any computer.Contact:Medical University of Lodz, 90–419 Lodz, POLAND, 4 Kosciuszki Avenue, Rector’s Office, phone 0048 42 272 59 66 umed.lodz.pl

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Issue with opening freeview
by Eunbi Kwon 07 Sep '21

07 Sep '21

External Email - Use Caution Hello, I'm using freeview version 7.2.2 on my macOS Catalina (version 10.15.6), and there has been a consistent issue with opening freeview where I get an error message "freeview quit unexpectedly." (I've attached the screenshot) I tried re-registering for freesurfer to replace the license file, but the issue persists. Please let me know how to resolve this issue. Thank you.

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FreeSurfer Visualization Questions
by Junyeon Won 06 Sep '21

06 Sep '21

External Email - Use Caution Dear Freesurfer experts, Could I have a couple of questions regarding visualization? 1) I found significant clusters on the right hemisphere volume after glm_fit and cluster correction. I would like to extract the volume from this cluster for each participant. According to the freeview instruction ( https://secure-web.cisco.com/1WRlFruYs_qR7muzrjF79S4e7sBuB1ehkXj2GwiMajz3IA…) the FSGD file (y.fsgd) should be loaded and select a point by clicking on the parametric map at that vertex to generate a plot for a particular vertex. I tried this but I am wondering if the mean value from the cluster can be extracted for each participant. I want to extract the values from each participant not just view the values through the FSGD file for further analysis. 2) Could you please let me know if it is possible to show the p-value numbers on the color scale? Best, JW

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XL defect detected_how to resolve
by Koustav Chatterjee 06 Sep '21

06 Sep '21

External Email - Use Caution Dear Forum members, Could you please help me resolve the following issue? The recon-all.log file is also attached herewith. CORRECTING DEFECT 34 (vertices=29039, convex hull=8209, v0=118726) normal vector of length zero at vertex 121849 with 0 faces vertex 121849 has 0 face XL defect detected... Numerical result out of range Linux research1-HP-280-G3-MT 4.4.0-210-generic #242-Ubuntu SMP Fri Apr 16 09:57:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Thank you for your time, Regards, KC

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Freesurfer September 2021