Freesurfer

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30055 discussions

New Postdoc Position in Neuroimaging, Machine Learning and Multi-Omics
by Joana Braga Pereira 02 Feb '25

02 Feb '25

External Email - Use Caution Dear all, I am looking for a Postdoc to work in my group at Karolinska Institute, Stockholm, Sweden. In my lab, we combine brain imaging with different machine learning algorithms, including deep learning, genetic as well as proteomics data to understand the pathological processes that occur in aging and neurodegenerative diseases ( https://secure-web.cisco.com/1LUlrCNfOJC8OL4EHldDwGP7T9W7uza4Ymxk_a08ewCd0i… ). This project will be carried out under my supervision and it will involve analyzing cross-sectional and longitudinal imaging data, combining clinical measures and cerebrospinal fluid biomarkers, as well as writing manuscripts and presenting results in international conferences. The Postdoctoral fellow will have the opportunity to work in a friendly and dynamic environment, be involved in many projects, collaborate with group members on different studies, learn new skills, interact with researchers with different backgrounds and from other universities, analyze large datasets from well-characterized cohorts, and develop a wide network of international collaborations. The ideal candidate should have the following qualities: - A PhD in medicine, neuroimaging, computational science, physics, neuropsychology, statistics or a related field. - Experience in statistical techniques, programming, and scripting in MATLAB, Python, R or other softwares. - Experience with analysing structural MRI, DTI, fMRI and/or PET imaging analyses. - Experience with different softwares such as SPM, FSL, FreeSurfer, AFNI, etc. - Experience or interest in working with aging and/or neurodegenerative disorders, particularly Alzheimer’s and Parkinson’s diseases. - Good academic record with scientific publications in world-class journals The Postdoctoral studies will be performed for 1 year, with possible extension for an additional year. There are also possibilities for a longer appointment after this 2-year period. To apply please go to: https://secure-web.cisco.com/1ok0B7DUbYsJXi1NjZzPaNOHBZuTa6ULGIl596LY5teOHN… (Deadline: *20.Feb.2025*) Best wishes, *Joana B. Pereira *| Associate Professor The Department of Neuroscience | Karolinska Institutet Nobels väg 9 | 171 65 Stockholm, Sweden joana.pereira(a)ki.se | ki.se <https://secure-web.cisco.com/1PAHM_fefVciSDCBLAjCTm7kotIxcHPIqK-gYp4qTnUD5E…> https://secure-web.cisco.com/1IE_fPDOvKF_Zs5nP-OSDvgZTUsRi2WJ6vfIFcUNmpfdaW… <https://secure-web.cisco.com/1HGoWCTPZ3hTpT9zbrri2MXrmnONkglfaBxascflJUMOnv…> ______________________________________ Karolinska Institutet – a medical university

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Re: [Freesurfer] help with freeview - could not connect to display :0 This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
by fsbuild 02 Feb '25

02 Feb '25

External Email - Use Caution  Did you try the different settings for DISPLAY as shown on this wiki page ?https://secure-web.cisco.com/1JJ6w3J3qDoL-kbM7jeWcvxRNbfeldJYCS4Fmq-CcyRIOy49TROE3oTOihjqrxlz5uJC9AIlqRFptB8848W3MhA65fHNbtKdhaZNcT6HuvOLH2Ev319sfrcFuYtVHV83uC8-RpLe37xKDoVlNkq_K4jyNstu_1KsesDqfiycLcVZJrYSPAaRKH3dFLhWTVbQ509gM5umBhlcph533uq9eBLGH_xsX8qGqfYmE1DLVZ7YK0kKlCBMNfFV5BAssftepwhRDz6ccqs5-_lcXwcTeOVFCpgqyeMN2P8IopcguQiwqzIxVdUPC8SRseNzk41VMMl4p8L_hIb9oh3NYUFw3bQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu Before trying to run freeview, you could try running a test X-Windows program like glxgears $ sudo apt install mesa-utils$ which glxgears/bin/glxgears$ glxgears If your WSL environment is setup correctly to communicate with the X-server running on the Windows host, then you should see a window displaying running gears. Besides Xming - which some people have not been able to get to work - you could also try MobaXterm or VcxSrv instead for X-Windows servers.  There are links to those on the above wiki page. - R.. On Feb 1, 2025, at 11:43, Paola Di Filippo <paola.difilippo(a)unifg.it> wrote:        External Email - Use Caution        hi everyone,i have succesfully managed to install freesurfer on my windows computer, with WSL2 and UBUNTU 22.04.when i open ubuntu this is what i get: -------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /usr/local/freesurfer/7.4.1 FSFAST_HOME       /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjects MNI_DIR           /usr/local/freesurfer/7.4.1/mni paolasofia@OR5909:~$ then when i try to launch freeview, this is what i get:paolasofia@OR5909:~$ freeview could not connect to display :0 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 i have installed freesurfer on my laptop following the same instructions, the ones on freesurfers website, and freeview is working fine. I searched online for suggestions and solutions but I can't seem to be able to solve the problem. i have tried it all, i am desperate. I hope somebody can help me. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1gSy8mc4q8AMG4kmwfzj8r7W7mF_Bj5gSc8pb4HwzL3_6a…

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help with freeview - could not connect to display :0 This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
by Paola Di Filippo 01 Feb '25

01 Feb '25

External Email - Use Caution hi everyone, i have succesfully managed to install freesurfer on my windows computer, with WSL2 and UBUNTU 22.04. when i open ubuntu this is what i get: -------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni paolasofia@OR5909:~$ then when i try to launch freeview, this is what i get: paolasofia@OR5909:~$ freeview could not connect to display :0 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 i have installed freesurfer on my laptop following the same instructions, the ones on freesurfers website, and freeview is working fine. I searched online for suggestions and solutions but I can't seem to be able to solve the problem. i have tried it all, i am desperate. I hope somebody can help me. --

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[WARNING: ATTACHMENT UNSCANNED]Issue with mris_make_surfaces generating Incorrect pial surface
by 韦亚辉 31 Jan '25

31 Jan '25

External Email - Use Caution Dear FreeSurfer, I have modified some processing steps in NHPPipeline, but I am encountering an issue with the mris_make_surfaces command. Specifically, the pial surface generated appears correct in one half but incorrect in the other half. I have checked the required input files (aseg, filled, wm, T1, white surface), and they all seem fine. However, the issue persists. Here is the command I used: VARIABLESIGMA="12" MAXTHICKNESS="-max 15" PSIGMA="-psigma 7" NSIGMA_ABOVE="-nsigma_above 12" NSIGMA_BELOW="-nsigma_below 12" MINGRAY="-min_gray_at_csf_border 10" MAXGRAY="-max_gray_at_csf_border 20" mris_make_surfaces -variablesigma $VARIABLESIGMA $PSIGMA $MAXTHICKNESS $MINGRAY $MAXGRAY \ -white NOWRITE -aseg aseg -orig white.deformed -filled filled -wm wm \ -sdir $SubjectDIR -T1 $T1wHires $SubjectID lh -hires I have attached the necessary input files and results for your reference. Could you please help me identify the possible cause of this issue? Best regards, yahui

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Re: [Freesurfer] infantFS: expected outputs
by Zoellner, Frank 31 Jan '25

31 Jan '25

External Email - Use Caution Hi, I have another question. I set ccseg option to get CC stats but they do not show in the final aseg.stats file though it seem that the CC segemntnation is performend ? Yours Frank ---------------- adj. Prof. Dr. Frank Zoellner Acting head Computer Assisted Clinical Medicine Mannheim Institute for Intelligent Systems in Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner(a)MedMa.Uni-Heidelberg.de<mailto:Frank.Zoellner@MedMa.Uni-Heidelberg.de> Web: https://secure-web.cisco.com/1m0Kj20FyM86PUSYrf0HbRKDAEbErELxTGijhcN-gjE85P… Von: <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von "Zollei, Lilla,Ph.D." <LZOLLEI(a)MGH.HARVARD.EDU> Antworten an: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Datum: Donnerstag, 24. Oktober 2024 um 03:59 An: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] infantFS: expected outputs Dear Frank, You are correct. The list of segmentation labels is not 100% the same. For the infantFS segmentation labels you can refer to Table 1 in https://secure-web.cisco.com/1yiUa1Vk5ihTnaFGWa_rpomMezNViMShkgspNV0lMBe5DL… Best, Lilla ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Zoellner, Frank <Frank.Zoellner(a)medma.uni-heidelberg.de> Sent: Monday, September 23, 2024 4:31 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] infantFS: expected outputs External Email - Use Caution Dear Lilla, Besides the differences in the files, when looking at the segmentations we wondered why there are some labels zero in the aseg stats file. These are : Left-Inf-Lat-Vent CSF Right-Inf-Lat-Vent Brain-Stem Left-vessel Left-choroid-plexus Right-vessel Right-choroid-plexus 5th ventrikel WM-hypointensities We also did a cross check and had run the same subject with the normal freesurfer pipeline and here there have been segmentations for the above structures. Maybe you have an idea what is happening here ? or are these not included in the atlas? Thanks in advance Yours Frank ----------- adjunct Prof. Dr. Frank Zoellner Acting head Computer Assisted Clinical Medicine Mannheim Institute for Intelligent System in Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835121 Fax: +49 (0)621 3835123 Email: Frank.Zoellner(a)MedMa.Uni-Heidelberg.de<mailto:Frank.Zoellner@MedMa.Uni-Heidelberg.de> Web: https://secure-web.cisco.com/1m0Kj20FyM86PUSYrf0HbRKDAEbErELxTGijhcN-gjE85P… Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> Im Auftrag von Zollei, Lilla,Ph.D. Gesendet: Sonntag, 22. September 2024 16:12 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] infantFS: expected outputs Hi Marlene, This is correct. Even though infant_recon_all is trying to mimic the output folder structure and follows the FreeSrufer naming convention, it does not generate all of the files that the adult version does. Lilla ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Marlene Staginnus <ms2290(a)bath.ac.uk<mailto:ms2290@bath.ac.uk>> Sent: Monday, September 16, 2024 9:57 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] infantFS: expected outputs External Email - Use Caution Dear FreeSurfer Team, Apologies in case I missed this elsewhere, but I was wondering whether there is any information on what the expected outputs of running infant_ recon_all are, similar to this (https://secure-web.cisco.com/1842_5uJLUmhL9zjqueT9IG-O2ijdmDUyVixpX5UWMvoZ6…) for the adult pipeline? I am asking as after testing the pipeline using the example participant provided on openneuro (https://secure-web.cisco.com/1ZFwVrUQPg9OdHj5xfWvCvA6li9k0cO4hetJ6og0O1nRrJ…, I’ve noticed that some of the output differs from the adult version and I wanted to ensure that everything is running correctly before applying it to our data. For example, there is no ‘orig’ subdirectory or orig.mgz file in the ~/mri folder. Similarly, fewer files are included in the ~/stats folder (only: brainvol.stats, lh.aparc.stats, rh.aparc.stats) although I was able to able to generate other files (e.g., aseg.stats) using mri_segstats. Overall, only the following folders are generated following recon-all without errors: label, log, mri, stats, and surf. Is this correct or might there be something going wrong on my end? 1) FreeSurfer version: infant-dev-4a14499-20210109-4a14499 2) Platform: CentOS release 7 3) uname -a: Linux fhpc-1840 6.8.0-40-generic #40~22.04.3-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 30 17:30:19 UTC 2 x86_64 x86_64 x86_64 GNU/Linux 4) infant_recon_all log: see attached Thank you in advance! Best wishes, Marlene

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Corpus Callosum Missing in SAMSEG Output
by Taghizadeh Mortezaei, Nima 30 Jan '25

30 Jan '25

Dear FreeSurfer Support Team, I am using FreeSurfer version 7.4.1 and recently ran SAMSEG on a subject’s MRI data. However, I noticed that the corpus callosum does not appear as a distinct label in the segmented structures. After reviewing the output files and label definitions, I was unable to find any explicit segmentation for the corpus callosum in the SAMSEG results. Could you please clarify if the corpus callosum is included as a distinct structure in the default SAMSEG atlas? If not, is there a recommended approach to extract or segment the corpus callosum using SAMSEG? Any guidance or suggestions would be greatly appreciated. Please let me know if additional details or files are needed for context. Thank you for your time and support. Best regards, Nima Taghizadeh

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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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