Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

Regarding Freesurfer for Ubuntu 24.01
by Debika Ghosh 05 Feb '25

05 Feb '25

External Email - Use Caution Dear team, I need to use Freesurfer and I am on Ubuntu version 24.01. Since I could not find the specific installation file for this version of Ubuntu, I tried installing the .deb file for Ubuntu 22. The installation process is not working because it is showing somy dependency related error. Could you please suggest what can be done in such an instance? Best regards, Debika Ghosh --

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Error in loading wmparc2diff.mgz
by Ramesh Babu 04 Feb '25

04 Feb '25

External Email - Use Caution Dear Expert, I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is; $ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz Please see the attached file and give your suggestions. Regards Ramesh

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Patlak PET/MRI
by Andrade Rey René 03 Feb '25

03 Feb '25

External Email - Use Caution Dear community, I have tried the tutorial for PETsurfer. I would like to ask some questions. 1) I have seen in the tutorial when you do PVC correction it is done on PET dynamic raw data. Is this correct? Because I have seen some tutorial where it is suggested on the motion corrected by AFNI image so called pet.mc.nii.gz 2) I also would like to compute hypometabolism on epileptic patients based on a dynamic PET so called Patlak Kinetic modeling. Is that possible with Freesurfer? I know there is Qmodeling toolbox in SPM but I cannot get access to their toolbox (some issue about the download) and I don’t know if there is another workaround. If not possible to do Patlak with FreeSurfer is it correct to assume the mean of the dynamic PET will provide epileptogenic zone for epileptic patients based on FDG-PET as hypo metabolic regions? Sincerely, Rene Andrade.

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Automated extraction of dural/meningeal ROI
by Sneha Pandya 03 Feb '25

03 Feb '25

External Email - Use Caution Dear Doug, We are working on PET images and our tracer has a lot of non-specific binding close to meninges. To do so we want to be able to mask out meninges and other areas outside the brain. Following up on your suggestion as in https://secure-web.cisco.com/1Ae5FkdxMKpYB4bvu5-OiOws53J6bGdKfXI6vjilmtNuqX… thread we are planning to extract meninges ROI and mask it out from our PET image. What labels should we include from the aseg.mgz and gtmseg.mgz file to be classified as "brain". We want to compare our regional PET uptake with PVC'ed PET data as well hence gtmseg.mgz. Thank you, Sneha

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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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