Freesurfer February 2025

freesurfer@nmr.mgh.harvard.edu

48 participants
82 discussions

Re: [Freesurfer] recon-all failed with FreeSurfer v8.0.0 (beta) on Mac
by fsbuild 06 Feb '25

06 Feb '25

External Email - Use Caution  The fix for the error you posted when running the 8.0.0 beta release - which has to do with how some python code is run - will be fixed in the forthcoming 8.0.0 release; it’s unrelated to your environment setup. The commands that run the recon-all pipeline in the 8.0.0-beta 2024 release have changed since the older 7.2.0 release from 2021, so 7.2.0 does not reproduce that error.  You could try setting the environment variable listed below on your 8.0.0-beta recon-all command line (bash shell example) to revert to the older recon-all behavior. $ export FS_V8_XOPTS=0 && recon-all <your arguments here> - R. On Feb 6, 2025, at 01:02, Lee Lin <lee.kevin.lin(a)gmail.com> wrote:        External Email - Use Caution        Dear FreeSurfer developers, running the 8.0.0-betaRecently, I attempted to run FreeSurfer on my new work computer (MacBook Pro, Apple M3 Max, macOS 14.6). I found that v8.0.0 beta is the only compatible version, and the installation appeared to be successful. However, when running recon-all on my 7T anatomical data using the following command:recon-all -i <path_to_anatomy_nii_file> -s <subject_initials> -allI encountered an error during subcortical segmentation (see attached "7T_recon-all.log" and screenshots). It looks like the deep learning model used by mri_sclimbic_seg was reporting an input dimension mismatch.  To diagnose the issue, I tested the following possibilities:1. Is the error specific to this data?I ran recon-all on other 7T anatomical data, but the same error occurred.2. Is the error specific to 7T data?I tested recon-all with 3T data, but in this case, the process was killed even earlier, and no useful error message was provided (see "3T_recon-all.log"). I’m unsure whether these two issues are related..3. Is the issue related to the FreeSurfer version or my work environment?I ran recon-all on an older MacBook Pro (Apple M1, macOS 12.6) using FreeSurfer 7.2.0, and the process completed successfully. This suggests that the issue is specific to FreeSurfer v8.0.0 beta or my work environment rather than the dataset itself. Do you have any suggestions on this issue? Additionally, I noticed that FreeSurfer v8.0.0 beta uses a deep learning model for segmentation, which differs from previous versions. Is there a way to switch back to the traditional segmentation method? I would greatly appreciate any insights or troubleshooting suggestions. Best regards,Lee Lin<7T_recon-all.log><7T_recon-all_error-msg2.png><7T_recon-all_error-msg1.png><3T_recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1vJ3hkJcbeBmkSfHBn3idEPYXvTCSXvkeUXnJa1D_GXnUv…

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recon-all failed with FreeSurfer v8.0.0 on Mac
by Lee Lin 06 Feb '25

06 Feb '25

External Email - Use Caution Dear FreeSurfer developers, Recently, I attempted to run FreeSurfer on my new work computer (MacBook Pro, Apple M3 Max, macOS 14.6). I found that v8.0.0 beta is the only compatible version, and the installation appeared to be successful. However, when running recon-all on my 7T anatomical data using the following command: recon-all -i <path_to_anatomy_nii_file> -s <subject_initials> -all I encountered an error during subcortical segmentation (see attached "7T_recon-all.log" and screenshots). It looks like the deep learning model used by mri_sclimbic_seg was reporting an input dimension mismatch. To diagnose the issue, I tested the following possibilities: 1. Is the error specific to this data? I ran recon-all on other 7T anatomical data, but the same error occurred. 2. Is the error specific to 7T data? I tested recon-all with 3T data, but in this case, the process was killed even earlier, and no useful error message was provided (see "3T_recon-all.log"). I’m unsure whether these two issues are related. 3. Is the issue related to the FreeSurfer version or my work environment? I ran recon-all on an older MacBook Pro (Apple M1, macOS 12.6) using FreeSurfer 7.2.0, and the process completed successfully. This suggests that the issue is specific to FreeSurfer v8.0.0 beta or my work environment rather than the dataset itself. Do you have any suggestions on this issue? Additionally, I noticed that FreeSurfer v8.0.0 beta uses a deep learning model for segmentation, which differs from previous versions. Is there a way to switch back to the traditional segmentation method? I would greatly appreciate any insights or troubleshooting suggestions. Best regards, Lee Lin

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Re: [Freesurfer] Regarding Freesurfer for Ubuntu 24.01
by fsbuild 05 Feb '25

05 Feb '25

External Email - Use Caution  We are aware that changes to the system libraries in Ubuntu 24 prevent installing packages that installed and ran fine in Ubuntu 22.  We hope to have a development build available for Ubuntu 24 in the near future.    Ubuntu 22.04 LTS was made generally available in April of 2022 with the standard 5 year support cycle from Canonical - which means it has support until 2027.   Some users will not be eager to switch to the latest version of an OS if for example they started processing their subjects on Ubuntu 22 given that upgrading to Ubuntu 24 could change their results. - R. On Feb 5, 2025, at 04:47, Debika Ghosh <debika.2023phd(a)iimu.ac.in> wrote:        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  _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1VTbjASPeJpyBz8jnUW5skvvU-7OQD1y4_18-nynPuMULa…

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Re: [Freesurfer] mri_TumorSynth: command not found
by fsbuild 05 Feb '25

05 Feb '25

External Email - Use Caution  I think that command is no longer/not supported and its wiki page is out of date; it has not been in any 7.X or 8.X  freesurfer distribution dating back to at least 2020. - R.On Feb 5, 2025, at 12:40, Zapaishchykova, Anna <azapaishchykova(a)bwh.harvard.edu> wrote:mri_TumorSynth

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Fw: mri_TumorSynth: command not found
by Zapaishchykova, Anna 05 Feb '25

05 Feb '25

Hi, Hope this email finds you well. Just wanted to report that https://surfer.nmr.mgh.harvard.edu/fswiki/TumorSynth package gets "mri_TumorSynth: command not found" on freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc and on 7.4 Best, Anna

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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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Freesurfer February 2025