Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Identical values for different cingulate regions
by Taghizadeh Mortezaei, Nima 28 Jan '25

28 Jan '25

Dear FreeSurfer developers and community, I was reviewing the stats outputs of recon-all from multiple cases processed using FreeSurfer version 6.0.0, and I encountered an unusual issue. Unfortunately, I do not have access to the stats files, but based on the results provided in excel, I have noticed that the gray matter volumes for the caudal anterior cingulate and isthmus cingulate are identical within each hemisphere. (lh.caudal_anterior_cingulate = lh.isthmus_cingulate rh.caudal_anterior_cingulate = rh.isthmus_cingulate). Also, the white matter volumes for the isthmus cingulate are also identical between hemispheres (lh.isthmus_cingulate = rh.isthmus_cingulate). The consistent pattern across all cases and its limitation to the cingulate regions leads me to question whether this could be possible from an issue in the segmentation and parcellation processing, or if it might be due to errors during data transfer. I would appreciate your guidance. Please let me know if additional details or context would help clarify this matter. Thanks!

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Re: [Freesurfer] no Qt platform plugin could be initialized
by fsbuild 27 Jan '25

27 Jan '25

External Email - Use Caution  Please let us know which freeeusfer release you installed using the CentOS8 RPM file, e.g., as downloaded from https://secure-web.cisco.com/1pEbxYZrDQAhBusbNo8pVT0Cdze9IJw2Pdh5… you used the CentOS8 rpm installer for freesurfer 7.4.1 or an earlier release, then you will be using the Qt libraries included in the freesurfer distribution (and not what is installed on the system). If you installed the latest CentOS8 rpm package made from the development build as found under,https://secure-web.cisco.com/15Gu6EXjohneOqt4rIOWN3JkJ-j0PjpZ5j5BtaUC… then I think it will install whatever Qt packages are needed for use on the system.  You should not need to set the QT_QPA_PLATFORM_PLUGIN_PATH environment variable. - R. On Jan 23, 2025, at 22:12, Shakour Abuzneid <Shakour.Abuzneid(a)jefferson.edu> wrote:        External Email - Use Caution        I have installed freesurfer on RHEL8. When I try to run the freeview, I get the following error: 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, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb. Aborted (core dumped) Any idea how to fix this? I have done the following: export QT_QPA_PLATFORM_PLUGIN_PATH=$FREESURFER_HOME/lib/qt/pluginssudo yum install qt5-qtbase qt5-qtbase-devel  Thanks!  The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.  CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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no Qt platform plugin could be initialized
by Shakour Abuzneid 23 Jan '25

23 Jan '25

External Email - Use Caution I have installed freesurfer on RHEL8. When I try to run the freeview, I get the following error: 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, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb. Aborted (core dumped) Any idea how to fix this? I have done the following: 1. export QT_QPA_PLATFORM_PLUGIN_PATH=$FREESURFER_HOME/lib/qt/plugins 2. sudo yum install qt5-qtbase qt5-qtbase-devel Thanks! The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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longitudinal analyses, more than 2 timepoints
by Eszter Boros 23 Jan '25

23 Jan '25

External Email - Use Caution Dear FreeSurfer Team, We are analyzing some longitudinal data (baseline [0], 6 months, 1 year, 1.5 years) using FreeSurfer 7.4.1. We already analyzed two timepoints (basline[0] and 6 months) but now we are trying to look at 4 timepoints in total. I was wondering what the best way would be to do this. For the longitudinal processing, should we create 3 bases/within-subject templates between 0-6 months (this is already done), 0-1year, 0-1.5years), or between 0-6months, 6months-1year, 1year-1.5years. Or both? Also, is it okay to correct/edit only the bases? After the longitudinal processing, can we create a Longitudinal Table and apply the two-stage model (LongitudinalTwoStageModel) method? Or because of the 4 time points, we need to apply something else. Thank you for your help in advance! All the best, Eszter

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recon-all error
by 박경일 23 Jan '25

23 Jan '25

External Email - Use Caution Dear FS Development Team, I recently encountered an error while running the recon-all process. This is the first time I have experienced this issue with the routine recon-all procedure. Attached are the result logs from the same image file. One shows the recent error and the other is from the successful run I performed previously. Due to this error, I am unable to get any volume or thickness data in the stats folder. Thank you for your time and support. Best regards, KI Park

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[freesurfer] recon-all error
by 박경일 23 Jan '25

23 Jan '25

External Email - Use Caution Dear FS Development Team, I recently encountered an error while running the recon-all process. This is the first time I’ve experienced an issue with this routine process. Please refer to the attached recon-all log file for detailed information regarding the error. Thank you for your time and support. Best regards, KI Park

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aseg.mgz file not generated after recon-all
by Sara Rapuc 23 Jan '25

23 Jan '25

External Email - Use Caution Dear all, I ran FS recon-all -subcortseg -sd -subjid and it was completed without any errors. However, when looking into the mri folder, there is no aseg.mgz file, only aseg.auto.mgz. Could you please explain why this is and how to get the aseg.mgz file? Thank you. Best wishes, Sara

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Recon-all error...
by 박경일 23 Jan '25

23 Jan '25

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Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data
by Michael Eyre 23 Jan '25

23 Jan '25

External Email - Use Caution Hi, thanks for your response, apologies for late reply. nu.mgz looks fine When I run tkregisterfv --s subject --fstal : orig.mgz(mov) is pretty well aligned to mni305.cor.mgz(targ) - images attached As you can see there is some signal dropout in the inferior temporal lobes but this is not unusual for 7T acquisitions, my other subjects have run without problems. thanks Mike Eyre ________________________________ From: Michael Eyre Sent: 11 January 2025 21:21 To: dgreve(a)mgh.harvard.edu <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data Hi, thanks for your response, apologies for late reply. nu.mgz looks fine When I run tkregisterfv --s subject --fstal : orig.mgz(mov) is pretty well aligned to mni305.cor.mgz(targ) - images attached As you can see there is some signal dropout in the inferior temporal lobes but this is not unusual for 7T acquisitions, my other subjects have run without problems. thanks Mike Eyre

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Re: [Freesurfer] Freesurfer crashing (gui) or exting with error (command line)
by fsbuild 23 Jan '25

23 Jan '25

External Email - Use Caution  You don’t have permission to write to the default location of SUBJECTS_DIR as set in the freesurfer shell environment, i.e., /Applications/freesurfer/7.4.1/subjects.  The example subject data there is on purpose meant to be read only along with the rest of the freesurfer installation.  When it comes time to process your own subject data and write new or modify existing files, then you should set SUBJECTS_DIR to a path you always have write permission to, e.g., in your home directory,  $ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects… place your data under $HOME/subjects and run your freesurfer/freeview commands .... - R. On Jan 23, 2025, at 06:00, Claas Philip Nähle <cp(a)naehle.net> wrote:        External Email - Use Caution        I am trying to create a 3D brain model from a *.nii file (here: test.niiI), which I have copied to the subjects folder. A) Using the command line, the following error messages appear: Phils-MacBook:~ cnaehle$ recon-all -s brain -all -i /Applications/freesurfer/7.4.1/subjects/test.niimkdir: /Applications/freesurfer/7.4.1/subjects/brain: Permission deniedfs-check-version --s brain --o /var/folders/xz/ydj4gf611v5gynjdql0mqzwr0000gn/T//tmp.8jh0SIERROR: cannot find brainrecon-all: version check failedfs-check-version --s brain --o /var/folders/xz/ydj4gf611v5gynjdql0mqzwr0000gn/T//tmp.8jh0SI Phils-MacBook:~ cnaehle$  With:Phils-MacBook:~ cnaehle$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1Phils-MacBook:~ cnaehle$ export SUBJECTS_DIR=$FREESURFER_HOME/subjectsPhils-MacBook:~ cnaehle$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.4.1FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjectsMNI_DIR           /Applications/freesurfer/7.4.1/mni Now, since this is for a 4th grade project for my daughter, it would be great if you could assist me. 1. Permssion denied: I have grant full disc access to Freesurfer and the terminal, but still….2. Error cannot find:  My Understanding is, that -s specifies the desired name of the output file, i. e. It will be created?3. Version check failed: No idea. B) Using the GUI, Freesurfer simply crashes. The crash log report is rather long as usual, but I can easily provide it if necessary. The Nifti file was created from DICOM images using Micron. Any advice would be greatly appreciated. Regards  Philip ------- Prof. Dr. Claas Philip Nähle cp(a)naehle.net +49-178-4001619 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1diz10loniHrO26jrUXhHQcZMRcpC86rmU8ogQ0yU3DutF…

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