Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Problem with mri_glmfit
by Monami Nishio 19 Oct '23

19 Oct '23

External Email - Use Caution Dear whom may concern Hello Freesurfer Developers, I recently ran the mri_glmfit-sim command to replicate a previous PhD student's result, and found out that his output and mine are different, although the code and input is exactly the same. The previous PhD student ran the code in 2022 April, and I ran it in 2023 October. This is the exact command I run mri_glmfit-sim --glmdir data/ses-0${timepoint}/${hem}_MM_${variable}_n31_ fwhm_src5trg5.glmdir/ --perm 1000 $sig abs --perm-resid --cwp 0.05 --2spaces; According to the log, the difference is in the simulation section, this is his log (2022.04.log) Starting simulation sim over 1000 trials mri_glmfit simulation done 42.124 this is mine (2023.10.log) Starting simulation sim over 1000 trials INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry().... mri_glmfit simulation done 27.9102 I attached log files for each to this email. I searched for what "INFO: MRImask() using MRImaskDifferentGeometry()" means in FreeSurferWiki, but I can't find any answer. Could you let me know if there are any updates about this command recently? 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 2) Platform: Linux version 3.10.0-1160.21.1.el7.x86_64 ( mockbuild(a)kbuilder.bsys.centos.org) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC) ) Sincerely, Monami

2 1

Removeing the email
by Hânieh Mohammadi 18 Oct '23

18 Oct '23

External Email - Use Caution Hello, Please remove my email: hanieh.bme(a)gmail.com from the Freesurfer mailing list. Thank you -------------------------------- Hânieh Mohammadi , Ph.D (she/her) Postdoctoral researcher in Biomedical Engineering EPIC Center of the Montreal Heart Institute 5055 Rue Saint-Zotique, Montreal, Quebec H1T 1N6

1 0

lta_convert issue with ants Registration Matrix
by Yazdan Rezaee Jouryabi 18 Oct '23

18 Oct '23

External Email - Use Caution Dear all, Hi for checking registration i used fsl applyxfm on an Image(1)(Called Image.nii ) with specific Registration Matrice (Which we suppose to receive when we apply registration Methods) and Generate the "fsl_resampled.nii.gz" (Note: Image Orientations were LAS and in one other Experiment with also the same problem PSR) for our case i will attach the "fsl.mat" (Desired Matrix) using, fsl, freesurfer, and ants i got the correct results (let's call them "fslregistered.mat" and "freesurfer.mat" the converted lta to fsl-liked Matrix) Everything is OK till now But the converted lta-like and fsl-like matrix for ANTs (Which are called ants.lta, and ants.mat) using the lines below: - ConvertTransformFile 3 ./ANTS/ants_0GenericAffine.mat ./ANTS/ants.txt - lta_convert --initk ./ANTS/ants.txt --outlta ./ANTS/ants.lta --src ./Image.nii --trg ./fsl_resampled.nii.gz --ltavox2vox - lta_convert --inlta ./ANTS/ants.lta --outfsl ./ANTS/ants.mat --src ./Image.nii --trg ./fsl_resampled.nii.gz As All Results Images (Registered Image of all Methods) are aligned perfectly i think that there might be some issues with lta_convert Best Regards Yazdan Rezaee J *P.S. *" I've checked the one similar mail on this topic and the conclusion on that was about (sform, qform) incompatibility but the affine matrices of S-form and q-form are equivalent in my case."

2 6

Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.
by Lawless, Dylan 18 Oct '23

18 Oct '23

External Email - Use Caution Hello, I am attempting to create a freesurfer v7.2.0 docker container that can run tracula on the freesurfer outputs, however, I am unable to get past the intra-subject registration step without receiving the following error: --s sub-01 --mov /home/dylan/Documents/TRACULA /OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.464939/template.nii --reg /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.464939/reg.init.dat --niters 1 --maxangle 90 --tmp /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.464939/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov fslregister 7.2.0 dylan-virtual-machine Linux dylan-virtual-machine 6.2.0-32-generic #32~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Aug 18 10:40:13 UTC 2 x86_64 GNU/Linux nIters 1 if: Expression Syntax. ERROR: cannot find /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask Linux dylan-virtual-machine 6.2.0-32-generic #32~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Aug 18 10:40:13 UTC 2 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Oct 6 09:08:11 EDT 2023 Here is a link to the github page I am using for my custom dockerfile: https://secure-web.cisco.com/1p9u2_NBbOAc0qnjlGxSllp_ZZuxw7-lwoxYpC_WEQDib2… I used neurodocker to combine installations for FSL and Freesurfer. I am using FSL v6.0.0 and Freesurfer version: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b. The log output contains the same information as the code linked above. Machine info: uname -a Linux dylan-virtual-machine 6.2.0-32-generic #32~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Aug 18 10:40:13 UTC 2 x86_64 GNU/Linux I have also attached the config file I have created for this test dataset.

2 8

FreeSurfer License
by Camille Fakche 17 Oct '23

17 Oct '23

External Email - Use Caution Dear FreeSurfer community, I would like to obtain a free license to use FreeSurfer, I hope I am sending the request in the right place. Thank you, Camille. -- FAKCHE Camille Post Doctoral Researcher Centre for Human Brain Health (CHBH) University of Birmingham, UK

2 1

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
by Marina Fernández 17 Oct '23

17 Oct '23

External Email - Use Caution Hi Andrei, I was referring to .bashrc file located in these directories: /root/.bashrc /home/'your_user'/.bashrc

1 0

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
by fsbuild 17 Oct '23

17 Oct '23

External Email - Use Caution From what I can see, the freesurfer release 7 installers do not modify the shell init file, e.g., bashrc, and neither did the VM provided in the past with freesurfer 7.2.0 pre-installed have an entry with FS_DISABLE_LANG set in the bashrc file. - R. On Oct 17, 2023, at 06:04, Marina Fernández <marina.fdez.alvarez(a)gmail.com> wrote:        External Email - Use Caution        Hi Andrei and Freesurfer experts,We had the same problem in the past and we noticed there was an extra line in the .bashrc file of Ubuntu: export FS_DISABLE_LANG="true"Deleting this line solves the problem. The .bashrc file should contain only the following FS lines:#Freesurfer:export FREESURFER_HOME=/usr/local/freesurfersource $FREESURFER_HOME/SetUpFreeSurfer.shMake sure you do this for home and root .bashrc files.Hope this helps.Best wishes,Marina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
by Marina Fernández 17 Oct '23

17 Oct '23

External Email - Use Caution Hi Andrei and Freesurfer experts, We had the same problem in the past and we noticed there was an extra line in the .bashrc file of Ubuntu: export FS_DISABLE_LANG="true" Deleting this line solves the problem. The .bashrc file should contain only the following FS lines: #Freesurfer: export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh Make sure you do this for home and root .bashrc files. Hope this helps. Best wishes, Marina

1 0

NIH : Training in Advanced Statistical Methods in Neuroimaging and Genetics, April 15-26, 2024, Salt Lake City
by ROBERT CARY WELSH 16 Oct '23

16 Oct '23

External Email - Use Caution Hi everybody, We are pleased to announce that the application portal is still open for the NIH funded 2024 session of the course, “Training in Advanced Statistical Methods in Neuroimaging and Genetics”. We hope you pass this email and the associate flyer on to your local neuroimaging community. The course will start on Monday, April 15, 2024 and finish on April 26, 2024. We are happy to announce that the course is to be held in person, in Salt Lake City, Utah, United States at the University Guest House Conference Center. Our course also includes an ongoing continuing education portion. The course is an intensive 2-weeks, about 8 hours per day of a mix of lectures and hands-on computer labs. neurostatsbootcamp.org<http://secure-web.cisco.com/1lY-GvKYuvPetRR2S18eLjaUgPJfCtRozXBiQs2RBMuhfjF…> The course cost is $3000 (see scholarship information below), which includes hotel accommodations at the Guest House (arrival on April 14 with departure on April 26), breakfast, lunch, day time snacks, three dinners out as a group, and the planned evening activities. All course attendees will arrange for their own transportation to Salt Lake City. The course cost does include a daily pass to the Salt Lake City Trax light rail/commuter system. (Please note that the course instructors' effort is supported by the NIH grant thus avoiding that cost being passed on to the course attendees. This course is strictly not-for-profit.) Because of the limited size and advanced nature of the course, attendance is by application only – please make sure to fully read the website instructions. In general, applicants must be a US citizen, permanent resident, or with an appointment at a US institution, though we do have the ability to accommodate 3 to 6 individuals that do not meet this criteria. We anticipate the total class size to be between 22 and 25 students. There are opportunities for scholarships which can partially offset hotel accommodations. These are based on true financial need and you will be instructed how to apply if you are admitted to the course. We look forward to seeing you in SLC in 2024! The application deadline is Nov 1, 2023. Decisions around Dec 5th. For more information email us at neurostats(a)g.ucla.edu<mailto:neurostats@g.ucla.edu> or advancedstatisticscourse(a)utah.edu<mailto:advancedstatisticscourse@utah.edu> Robert and Anna ------------------------------ Robert Welsh, PhD Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics rcwelsh(a)g.ucla.edu<mailto:rcwelsh@g.ucla.edu> robert.c.welsh(a)utah.edu<mailto:robert.c.welsh@utah.edu> Anna Docherty, PhD Associate Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics anna.docherty(a)utah.edu<mailto:anna.docherty@utah.edu>

1 0

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
by fsbuild 16 Oct '23

16 Oct '23

External Email - Use Caution Freesurfer 7.4.1 on Ubuntu 20 uses its own versions of Qt libraries and not the system versions.   So if your setup is looking for or finding system versions of those libraries, then freesurfer may be installed incorrectly and/or could be finding the wrong Qt libraries via use of environment variables like LD_LIBRRY_PATH or Qt*.  (I would try not to set LD_LIBRARY_PATH and Qt environment variables in your shell environment before source’ing the freesurfer setup script). I suggest you remove whatever freesurfer distribution you have on the machine and do a clean re-install of 7.4.1 using the .deb package installer which you can download via the link, https://secure-web.cisco.com/1__PHy5riz1krqgipNavAJIc6annOjWAPD9… If freesurfer was previously installed with the linux package tools then it should work to uninstall it with,$ sudo apt remove freesurfer… answer y to all prompts ... If you unarchived the *.tag.gz file somewhere then “rm -rf” should work on the root freesurfer directory. With the previous freesurfer installation removed, cd to where you downloaded the freesurfer_ubuntu20-7.4.1_amd64.deb and try, $ sudo apt-get -y install ./freesurfer_ubuntu20-7-dev_amd64.deb… wait for install to finish … $ cd$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 ————Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /usr/local/freesurfer/7.4.1FSFAST_HOME       /usr/local/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjectsMNI_DIR           /usr/local/freesurfer/7.4.1/mni $ which freeview /usr/local/freesurfer/7.4.1/bin/freeview$ freeview… freeview should open an empty window … … quit freeview and try opening this example volume … $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz  If you see the attached image, then freeview/Qt is essentially working. - R. On Oct 14, 2023, at 14:14, Andrei Bieger <andreibieger(a)gmail.com> wrote:        External Email - Use Caution        Hi, all!I had to reinstall my VM where I had freesurfer running. Everything was running fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows laptop, where I'm running the version 7.4.1 of Freesurfer.When I downloaded freesurfer it wouldn't run freeview, with the following output: "Application failed to start because no Qt platform plugin could be initialized. Available plugins are: (...)"After some research, I tried "sudo apt install qt5-default" and freeview started running. But the thing is, every time I try loading a subject, the surfaces get completely misaligned with the volumes and the following messages show on the terminal: "Warning: MatrixInverse failed" and "Did not find any volume info". Please, see attached image.<Screenshot from 2023-10-14 15-06-44.png>I tried using Ubuntu 22 and previous versions of freesurfer but the problem persisted. I also found a message with a similar issue on this list, but the user stopped answering so a solution wasn't proposed. There is also a release note from v5.3.0 saying that on Fedora this message would come up, but this is not the case.Any help with that?-- Andrei Bieger_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

4 8

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer