Freesurfer April 2025

freesurfer@nmr.mgh.harvard.edu

40 participants
53 discussions

Guidance on SegmentHA with Low-Res MRI
by Taghizadeh Mortezaei, Nima 04 Apr '25

04 Apr '25

Dear FreeSurfer Community, I’m currently working with clinical MRI data and would appreciate your guidance regarding two issues I'm encountering with hippocampal/amygdala segmentation (segmentHA_T1.sh script). My available T1w and T2w scans both have 6 mm slice thickness and are anisotropic and I/m working with FreeSurfer 7.4.1. Given the slice thickness and anisotropy, is it advisable to use recon-all-clinical instead of the standard recon-all as a preprocessing step? I understand that the segmentation scripts depend on the subject having a full recon-all directory, but I’m unsure whether recon-all-clinical can serve as an alternative for this purpose or if the standard recon-all is strictly required for compatibility with the hippocampal segmentation pipeline. Would including the T2 scan be helpful if it has the same 6 mm slice thickness and anisotropic resolution as the T1? Thank you very much for your time and help. Best, Nima

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synthstrip use as a Docker for all MRI files in directory
by Sanchez Fernandez, Ivan 04 Apr '25

04 Apr '25

External Email - Use Caution First of all, thank you for developing freesurfer and synthstrip. They are wonderful tools. I am doing research with brain MRIs and part of the preprocessing needs skull stripping. Synthstrip is great. What I am trying to do is to create a Docker image that runs through all the MRI files in a directory and skull strips them with synthstrip. I thought this would be easy. My multistage Dockerfile looks like this, but it does not work because it does not recognize the command in the loop freesurfer/synthstrip -i "$file" -o "$file" or mri_synthstrip -i "$file" -o "$file" I guess that I do not know how to call a particular command within a unix loop. #########STAGE 1: CREATE THE MOUNT AND COPY THE MRIs TO BE SKULL-STRIPPED######### # Use ubuntu as base image FROM ubuntu AS prepare # Set working directory WORKDIR /app # Copy all MRIs COPY . . #########STAGE 2: USE SYNTHSTRIP######### FROM freesurfer/synthstrip # Set working directory WORKDIR /app # Copy all MRIs COPY --from=prepare . . # Create a loop that runs through the MRIs RUN for file in .; do freesurfer/synthstrip -i "$file" -o "$file"; done ENTRYPOINT ["ls"] Other option I thought about is to create a multistage build in which first I import the synthstrip program and then I loop through the MRI files and call synthstrip, but again I do not know exactly how to call the command to run synthstrip from python. Dockerfile #########STAGE 1: CREATE THE SYNTHSTRIP CONTAINER########### # Use synthstrip AS base image FROM freesurfer/synthstrip as builder # Set working directory WORKDIR /app #########STAGE 2: CREATE THE ANACONDA CONTAINER########### # Use miniconda as base image FROM continuumio/miniconda3 # Set working directory WORKDIR /app # Copy the initial image COPY --from=builder . . # Create the environment COPY environment.yml . RUN conda env create -f environment.yml # Make run commands use the new environment SHELL ["conda", "run", "-n", "app", "bin/bash", "-c"] # Code to run when the container is started COPY main.py . ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "app", "python", "main.py"] main.py file import os import subprocess for MRI in os.listdir('./file_with_MRIs'): print(MRI) proc = subprocess.Popen(['docker run freesurfer/synthstrip -i ', MRI, ' -o', MRI], stdin = subprocess.PIPE, stdout = subprocess.PIPE, stderr = subprocess.PIPE ) (out, err) = proc.communicate() print (out) Other option is to create a smaller Docker image that loops through the MRI files and just calls the synthstrip Docker image for each of those and collects the output, but I am not sure how to do that. Any suggestion or guidance highly appreciated. Thank you very much

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samseg: erroneous lesion labels on T2 red nucleus set to zero
by Simone Cauzzo 04 Apr '25

04 Apr '25

External Email - Use Caution Dear support I'm running the following command in Freesurfer 7.4: samseg --t1w ${SUBJECTS_DIR}/subjOPA${ss}/mri/orig/001.mgz --flair ${SUBJECTS_DIR}/subjOPA${ss}/mri/orig/oFL.mgz --t2w ${SUBJECTS_DIR}/subjOPA${ss}/mri/orig/oT2.mgz --s subjOPA${ss} --refmode t1w --pallidum-separate --lesion --fill --threads 16 --save-posteriors everything runs smoothly, but when I check the results I see some holes in the midbrain, in particular the red nucleus is labeled as csf. If I look at the T2.mgz file in the mri folder (I also run samseg2recon so I'm not sure it is the name given by samseg) I see that the red nucleus is set to zero, despite having non-zero values in the T2.norm.mgz volume. Two questions: 1) how can I avoid low-intensity T2 regions to be set to CSF? 2) is it possible to provide a brain mask to samseg if I already have a reliable one? Simone Cauzzo

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Re: [Freesurfer] synthstrip use as a Docker for all MRI files in directory
by fsbuild 04 Apr '25

04 Apr '25

External Email - Use Caution There is mri_synthstrip docker container available under,https://secure-web.cisco.com/11W4d_Wgaaf2feJLcp4xvaA9s4tjGSM9qFDeWi7g… See the documentation on this page under the section  (scroll down to) “SynthStrip Tool”,https://secure-web.cisco.com/1Vwi0RAuUuQeqS7OLv9IkFtVuAoZsGWAPulEVFxq… - R.

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Re: [Freesurfer] Freesurfer 7.4.0 not working in Ubuntu 24.04
by fsbuild 03 Apr '25

03 Apr '25

External Email - Use Caution  Ubuntu 24 is not yet listed as supported on the Freesurfer 7/8 release page,https://secure-web.cisco.com/1Y71zlCnT9l4FFrCeoLR086sxmpzf2-vsA1YN-VU1… We hope to have a development build running on Ubuntu24 in the next several months. I’m not sure what 7.X version it runs, but there is a freesurfer docker container available fromhttps://hub.docker.com/r/freesurfer/freesurfer/ Alternately, you could install VirtualBox, create and run a VirtualBox VM running Ubuntu 22 and install the 7.4.0 or 8.0.0 release .deb package into the VM.  It might be easier to use the VM instead of the docker container when running freeview because of the VM’s built in X-server.   There is write up on creating such a VM here,https://secure-web.cisco.com/1JpMcymxq0w-PnOS1WVlh9OZz2ckb1C_2KmbuGeSO… - R. On Apr 3, 2025, at 13:51, vittal korann <vittalkorann(a)gmail.com> wrote:        External Email - Use Caution        Hi Freesurfers, I updated my Ubuntu OS to 24.04 and successfully installed Freesurfer 7.4.0 in it. I am saying it was successful because I was able to open 'freeview' through the terminal.  However, the real problem started when I tried to execute the 'recon-all' command.  Moreover, I have seen a couple of similar threads on this issue (compatibility problem between freesurfer and Ubuntu 24.04) and the same link is pasted below.  1. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1NUkHGQewMEHgxfoI0FOHIYrPnPcv2TfkQhcry… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1d2Lq8eIGXm-ytCAot4wEj7UFCLuqQdJ5O4CN6… So, I am wondering whether this Freesurfer version supports the latest linux version or not? If not, I would appreciate it if somebody let me know the alternative ways of using it. Thanks in advance for your help!  RegardsVittal _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1787IxUigGPDTzv9Oo3y5e6Bwk9GREODNEs7phnBEm_z8p…

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Freesurfer 7.4.0 not working in Ubuntu 24.04
by vittal korann 03 Apr '25

03 Apr '25

External Email - Use Caution Hi Freesurfers, I updated my Ubuntu OS to 24.04 and successfully installed Freesurfer 7.4.0 in it. I am saying it was successful because I was able to open 'freeview' through the terminal. However, the real problem started when I tried to execute the 'recon-all' command. Moreover, I have seen a couple of similar threads on this issue (compatibility problem between freesurfer and Ubuntu 24.04) and the same link is pasted below. 1. https://secure-web.cisco.com/1svOIRTM9dlafSNLq9cR4qAfhog04NdsJtmKkMTcE2_x-K… 2. https://secure-web.cisco.com/1rtmIG1MiBse1Az5BA_1jyetPI0e-B6Vp3n6Jqh-W2kgSO… So, I am wondering whether this Freesurfer version supports the latest linux version or not? If not, I would appreciate it if somebody let me know the alternative ways of using it. Thanks in advance for your help! Regards Vittal

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Importing surface meshes from 3rd party cortical surface reconstruction tools for analysis in fsaverage template space
by James Hengenius 03 Apr '25

03 Apr '25

External Email - Use Caution Hi, I'm working with infant (0-30 month) MR data, and iBEAT ( https://secure-web.cisco.com/1T2WKIelhUu8n_wuNR_5gb37RydVg1xrWEVvlUOdcz2UFW…) is currently doing a better job than Infant FreeSurfer ( https://secure-web.cisco.com/1M3VIitCZu3azJ0yMsnC2UvSxSyhcRAkbfTg_v1IUkOJOb…) at cortical surface recon in this age range. However, I have custom surface ROI atlases on the fsaverage template and would very much like to leverage FreeSurfer's stats tools to map iBEAT subject surfaces to the template and extract stats from my custom ROIs. To do so, I need to - Bring my iBEAT VTK surfaces (~47K vertices per hemisphere) into FreeSurfer (mris_convert?) - Resample the meshes to FS surface resolution (~12.5K vertices per hemi) - Compute curvature stats on the iBEAT surfaces - Use mris_surf2surf (or equivalent) to map the resampled iBEAT surface to the fsaverage template using curvature - Compute/extract anatomical stats from the regions equivalent to the ROIs in my template space atlas. All of the above are presenting challenges. So far, I tried using mris_convert to bring the VTK into FS format, but when I tried using mris_anatomical_stats, I get errors. Note that I also ran InfantFS on the data, and that I copied the converted (but not downsampled) VTK pial surface from iBEAT to $SUBJECTS_DIR/$subjid/surf/lh.ibeat.pial > mris_anatomical_stats -log test.ibeat.log sub-0001 lh ibeat.pial outputting results to test.ibeat.log... reading volume /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/mri/wm.mgz... reading input surface /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.ibeat.pial... Using TH3 vertex volume calc Total face volume 58098.7 Total vertex volume 57390.1 (mask=0) reading input pial surface /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.pial... error: mrisReadTriangleFile opened /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.pial okay but surface doesn't match /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.ibeat.pial. nvertices:46854 != mris->nvertices:12240 || nfaces:93704 != mris->nfaces:24476 error: mrisReadTriangleFile failed. error: mris_anatomical_stats: could not read surface file /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.pial It appears this approach is failing due to a difference in meshes (the iBEAT mesh is at a different resolution, with more elements, than the lh.pial from InfantFS). Any tips for this and the other steps would be a big help! Thanks, Jim H. -- Jim Hengenius Research Associate Paus Research Group CHU Sainte-Justine Research Centre My Google Calendar <http://secure-web.cisco.com/1NyYdK1uBklqcDSsFMhBiedpJnPC-H6m83iYBtfLt-c-oKz…>

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Freesurfer Question - Pediatric pathology
by Stefanie Bradley 02 Apr '25

02 Apr '25

External Email - Use Caution Hi there, I'm working with MRI scans from children aged 3-6 years old. I was wondering if there's a way to integrate pediatric atlases into the Freesurfer recon-all pipeline? I'm also wondering if it's possible to integrate a lesion mask into the pipeline in the case of brain pathology? Thanks, Stef STEFANIE BRADLEY PHD CANDIDATE Holland Bloorview Kids Rehab Hospital 150 Kilgour Rd, Toronto, ON M4G 1R8 stefanie.bradley(a)mail.utoronto.ca [https://secure-web.cisco.com/1kWf2c8NzM8OclMTRcmltfW5rxRU9SRJI50sUcXDGlWqWx…]<https://secure-web.cisco.com/1uQzm_CoDmutDkOsJunQufG19PQx4c0AZhVnSO28l9XE9i…>

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Re: [Freesurfer] freesurfer 8
by fsbuild 01 Apr '25

01 Apr '25

External Email - Use Caution  The freesurfer_ubuntu22-8.0.0_amd64.deb installer may work if you are running an early version of Debian 12.  The system may refuse to do the install on the current version of Debian 12 because of system library conflicts.  I don’t see a container is currently available.  Another option would be to run an Ubuntu22 VM on your machine via virtualbox and install freesurfer there.  The VM is likely easier to use compared to the the container if you want to run the freeview image viewer.   There is a write up about creating a VM here,https://secure-web.cisco.com/10QGcnXeGUXgLlHRQsXLCaaMo-QzMvcEz4dlf1RcA… - R. On Apr 1, 2025, at 16:51, Gregory Book <gregory.a.book(a)gmail.com> wrote:        External Email - Use Caution        I'm attempting to run freesurfer 8 on debian 12. Are there any tips on making the Ubuntu package work on debian?orIs there a freesurfer 8 docker container out there?_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1Sn85p_MmVtQE68pcKYNp-8_KLB5cTUWlYD87srp-as4za…

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freesurfer 8
by Gregory Book 01 Apr '25

01 Apr '25

External Email - Use Caution I'm attempting to run freesurfer 8 on debian 12. Are there any tips on making the Ubuntu package work on debian? or Is there a freesurfer 8 docker container out there?

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