Freesurfer January 2025

freesurfer@nmr.mgh.harvard.edu

44 participants
67 discussions

Issue with Right Hemisphere Segmentation/Parcellation
by Taghizadeh Mortezaei, Nima 30 Jan '25

30 Jan '25

Hello FreeSurfer Developers and Community, I am working with an axial T1-weighted post-contrast MRI, with an original voxel size of 1×1×5.5 mm. I resampled this MRI in 3D Slicer using B-Spline interpolation and then saved it as a mgz file. After running recon-all on this resampled file, I noticed that the right hemisphere’s segmentation and parcellation are flawed. Also, considering the age and health situation of this patient, i believe the WM hypointensities are overestimated in the left hemisphere. I am using the following version of FreeSurfer: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460. The command line was: recon-all -s 12th_recon_output -i input.mgz -all -parallel -openmp 12 I’ve attached the recon-all log file, a screenshot from Freeview to illustrate the issue, and mri_info file. I would greatly appreciate any guidance, troubleshooting advice, or suggestions on what might have gone wrong and how to correct this issue. Thank you in advance for your help! Best regards, Nima

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Missing part of the pial surface
by FMU 29 Jan '25

29 Jan '25

External Email - Use Caution Hello everyone. I executed recon-all on an image, and it reconstructed the pial surface but left out a portion in the subcentral cortex area, as shown in the images. This is the first time I've encountered this issue. Could someone assist me in figuring out how to resolve it? I would be grateful for any help. Thank you, Mudathir

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FSL Team Research Software Engineer position in Oxford
by William Clarke 29 Jan '25

29 Jan '25

External Email - Use Caution We are looking for a Research Software Engineer to join the FSL development team at WIN. WIN conducts research in methods to acquire and model brain imaging data, including functional MRI, diffusion MRI, structural MRI and MR spectroscopy. WIN members have developed the widely used FMRIB Software Library (FSL), which enables the methods created within WIN to have a worldwide impact on the neuroimaging community. The post holder will work closely with MRI physics and analysis researchers to develop neuroimaging software aimed at neuroscientists and clinical researchers. They will be embedded in an existing, small but experienced team of research software engineers, forming the FSL team. The core duties will be software development activities to enhance existing software for widespread use, including building user interfaces for non-experts around core image processing tools, handling large datasets automatically, and specialist visualisation software. There is also scope for developing new software for neuroimaging analysis, contributing to ongoing and new research projects, building software test systems, and maintain existing software projects as required. This role involves interacting with software engineers, researchers, clinicians, and external end-users. Excellent communication skills and an interest in learning the foundations of neuroimaging are essential. This post is full time and fixed term until 30th November 2027. Only applications received via the University Jobs Website<https://secure-web.cisco.com/1yb7g_2pq3BE-wduWvKdXIWQrdJTwEJOPRK6gtMIej_Gtl…>, before 12:00 midday on Friday 28th February, will be considered. Key Responsibilities * Software development: Implementing new features and resolving operational problems within the FMRIB Software Library, which will require coding in a combination of Python, JavaScript, C++, and shell scripting. * Software support: Helping to resolve image analysis issues * Manage, deploy, and develop software using automated CI / CD pipelines. * Lead the development of appropriate and effective technical solutions and designs as required across various projects. * Take a lead role in the design, coding, testing and documentation of software. * Work with all researchers and other group members to further the impact of FSL-MRS and TIRL software. * Contribute to research publications and technical reports. Key Selection Criteria * Possess a doctoral degree in a relevant discipline, or hold a graduate degree with significant software development experience in a similar domain * Proficiency in the general-purpose programming languages, Python, and C++ or similar languages. * Proficiency in git and Gitlab/Github platforms for collaborative software development * Experience using and configuring automated CI / CD pipelines for testing and deployment * Excellent written and oral English communication skills * Ability to work well with others Will MR Spectroscopist & Wellcome Career Development Fellow WIN, University of Oxford

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FreeSurfer 8.0.0 beta error, while calculating the local gyrification index
by Katharina Wittfeld 28 Jan '25

28 Jan '25

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to compute the local gyrification index but unfortunately the calculations terminated with an error: recon-all -subject XXX -localGI -hemi rh FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc Platform used: Ubuntu 22.04.5 LTS From the log file: seg2cc --s XXX -rh seg2cc: update not needed. Run with --force-update to force an update Command exited with non-zero status 1 @#@FSTIME 2025:01:23:19:41:20 seg2cc N 3 e 0.05 S 0.01 U 0.04 P 103% M 2916 F 0 R 2820 W 0 c 1 w 51 I 0 O 0 L 20.43 20.49 19.84 @#@FSLOADPOST 2025:01:23:19:41:20 seg2cc N 3 20.43 20.49 19.84 Linux gt-psych.med.uni-greifswald.de 5.15.0-130-generic #140-Ubuntu SMP Wed Dec 18 17:59:53 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s XXX exited with ERRORS at Thu Jan 23 19:41:20 CET 2025 The data was preprocessed before with recon-all and completed without any error and I've run this on multiple individuals without any success. The same commands worked fine with former FreeSurfer versions (6.0 and 7.3.2). On the freesurfer mailing list I haven't detected this problem. I would be very greatful, if you have any idea how to run it in this new freesurfer version. Best regards, Katharina -- Dr. rer. nat. Katharina Wittfeld University Medicine Greifswald Department of Psychiatry and Psychotherapy Ellernholzstr. 1/2 17475 Greifswald Germany Tel. +49 3834 86 22166 e-mail:Katharina.Wittfeld@uni-greifswald.de

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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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Freesurfer January 2025