Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30130 discussions

Re: [Freesurfer] Freeview issue
by fsbuild 22 Oct '23

22 Oct '23

External Email - Use Caution   The Qt graphics libraries may need virtualGl over a remote X connection.  So try prefacing your freeview command with "vglrun".  See the introductory text about vglrun and the install commands on this page, https://secure-web.cisco.com/1_jeLuB9K3YFX-_vkUZquNAqePEbWUSsW-inupVmdbjXle… Then once the remote display of images is working, you might run into an issue trying to map the display size to your remote screen resolution. - R. On 10/22/23 03:57, yunus soleymani (soleymani.yunus(a)yahoo.com) wrote:         External Email - Use Caution         I did the following codes respectively:> cd> wget MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/11GVLnIDWxo_vR8D2Oa9AP0rLkOmLrhl51L-g0K4pY8mWN… > ls freesurfer_ubuntu22-7.4.1_amd64.deb > sudo apt-get update -y > sudo apt-get -y install ./freesurfer_ubuntu22-7.4.1_amd64.deb > export FREESURFER_HOME=/usr/local/freesurfer/7.4.1 > echo "export FREESURFER_HOME=/usr/local/freesurfer/7.4.1" >> $HOME/.bashrc > ls $FREESURFER_HOME > ls license.txt > echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc > echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc > echo "export DISPLAY=:0" >> $HOME/.bashrc > echo "source $FREESURFER_HOME/SetUpFreeSurfer.sh" >> $HOME/.bashrc  ..................................................................................................................................................... The above codes all worked correctly and the software was installed successfully. Also, the software analyzes the subjects correctly by using parallel recon-all code. The only issue is that the Freeview interface doesn't work and the error mentioned above appears. Is it because of that I am using a remote desktop connection tool to connect to my institute servers? --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be soleymani.yunus(a)yahoo.com+98 914 526 9298-------------------------------------------------------------------------------- On Sunday, October 22, 2023 at 11:12:08 AM GMT+3:30, fsbuild <fsbuild(a)contbay.com> wrote:         External Email - Use Caution         Wondering if you used the freesurfer_ubuntu22-7.4.1_amd64.deb installer package from the download page and installed it from your Downloads folder via,$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.debThe link for that file on the downloads page MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1P6sJsKdfjhSOlm7uHbTXJ8nsEFCHNYGKzdj0djukhVoPC… R.On Oct 22, 2023, at 02:19, yunus soleymani <soleymani.yunus(a)yahoo.com> wrote:        External Email - Use Caution        I have the same problem. I would greatly appreciate your help with this.--------------------------------------------------------------------------------Yunus SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical SciencesMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------On Saturday, October 21, 2023 at 12:24:10 PM GMT+3:30, Ramesh Babu <mgrameshbabu2013(a)gmail.com> wrote:        External Email - Use Caution        Dear Expert,Recently I installed the latest version of freesurfer in Ubuntu OS 22LTS.. Freesurfer is installed successfully, but freeview gives some errors which I pasted below. Please provide your suggestions. Thank YouRameshfreeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb.Aborted (core dumped)_______________________________________________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/1Z0_ffEGo83ss1m7kRMPeWTsWg7lKpmYawqoIi… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________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/1gxLJVkQyQWy-mN2IV23c0x-Z-B3Llabbuqf9fFBFx5T4K… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1CJwtL-NCVwbfYRfzulvtw0FqaswpVEEIEot84NQI4IAQZ… 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.

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Re: [Freesurfer] Freeview issue
by fsbuild 22 Oct '23

22 Oct '23

External Email - Use Caution  Wondering if you used the freesurfer_ubuntu22-7.4.1_amd64.deb installer package from the download page and installed it from your Downloads folder via, $ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb The link for that file on the downloads page https://secure-web.cisco.com/1_35_maf1qeyDwN-YbnCQ8jOb6jvY5lINnAz… - R. On Oct 22, 2023, at 02:19, yunus soleymani <soleymani.yunus(a)yahoo.com> wrote:        External Email - Use Caution        I have the same problem. I would greatly appreciate your help with this.--------------------------------------------------------------------------------Yunus SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical SciencesMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------On Saturday, October 21, 2023 at 12:24:10 PM GMT+3:30, Ramesh Babu <mgrameshbabu2013(a)gmail.com> wrote:        External Email - Use Caution        Dear Expert,Recently I installed the latest version of freesurfer in Ubuntu OS 22LTS.. Freesurfer is installed successfully, but freeview gives some errors which I pasted below. Please provide your suggestions. Thank YouRameshfreeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb.Aborted (core dumped)_______________________________________________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/1BZ4_HvToI5a6OuM5gIFWs2VyFinjkWLi8C5L5… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview issue
by Ramesh Babu 22 Oct '23

22 Oct '23

External Email - Use Caution Dear Expert, Recently I installed the latest version of freesurfer in Ubuntu OS 22LTS.. Freesurfer is installed successfully, but freeview gives some errors which I pasted below. Please provide your suggestions. Thank You Ramesh freeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb. Aborted (core dumped)

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Re: [Freesurfer] fsxvfb error: Falling back to using screens root_visual
by fsbuild 20 Oct '23

20 Oct '23

External Email - Use Caution I could be wrong, but it reads like those errors are from the libqt5xcb.so running into errors communicating with X windows.   Since freeview runs fine displaying those images on the machine when not exec'd thru fsxvfb, then maybe fsxvfb cannot capture because it is not expecting freeview to (still) run using Qt graphics and X-windows .  I believe the release notes say fsxvfb does not need an X-server and so perhaps it is trying to capture images directly from the graphics hardware.  Could be something is not up to date on your system with the graphics hardware drivers/system libraries. Another thing to consider is the freesurfer 7.4.1 release was not built for nor tested on Ubuntu 16 - the minimum version tested was Ubuntu 18.   Given you are running it from the path /usr/global/freesurfer/7.4.1 then I suspect you did not download and run the 7.4.1 debian package installer for Ubuntu 18 as recommended on the freesurfer download page,  https://secure-web.cisco.com/1pa_Juw1rvYdwKxiYGrhHioNA_vUa-3QRuSL2A9WRhRTgv… (which would install under /usr/local/freesurfer).   It would not be surprising for the Ubuntu 18 binary installer to fail trying to update an Ubuntu 16 system, but you could try running it.  You can decline/abort the installation if you don't approve of the system updates it reports are needed before installing freesurfer.  Even if the installer succeeds, we can't guarantee 7.4.1 will work correctly on Ubuntu 16. - R. On 10/19/23 17:50, Dani Del Rubin (rubinstd(a)ohsu.edu) wrote: QXcbConnection: XCB error: 1 (BadRequest), sequence: 167, resource id: 133, major code:

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HBT/FS60/CA segmentation
by Yasmine Salman 20 Oct '23

20 Oct '23

External Email - Use Caution Dear Freesurfer Developpers, When I look at the FreeSurfer documentation on hippocampal segmentation, I see that it is possible to obtain different segmentations in addition to the 'traditionnal ' freesurfer 7 one: - HBT: the hippocampus is subdivided into head, body and tail. - FS60: it mimics the FreeSurfer 6.0 hippocampal module, i.e. there is no head/body subdivision for the hippocampus. no head/body subdivision for hippocampal sub-regions. - CA: the "internal" labels (GC-ML-DG and molecular layer) are absorbed by the CA subfields. When I run the command line: segmentHA_T1.sh bert I get files: hipposubfields.lh.T1.v21.stats which contain the volumes of the freesurfer 7 segmentation but not the other segmentations. I would like to generate a .stat file (one/subject) of segmentation type 'CA' , how can I do this? Thank you, Best, Yasmine

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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

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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

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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."

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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.

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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

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