Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

cvs register error
by Xuesong Su 07 Apr '25

07 Apr '25

External Email - Use Caution Dear all, I am attempting to use my own data and follow the instructions on the petsurfer wiki. I ran the following command: `mri_cvs_register --mov 001 --template cvs_avg35_inMNI152` The output showed: [...] `mri_cvs_register: Step 1 (spherical registration) took 542 seconds` `surf2vol: Command not found.` It appears that Step 1 has been completed, but it's stuck on Step 2. So, I tried running: `mri_cvs_register --mov 001 --template cvs_avg35_inMNI152 --step2 --nocleanup` However, the output still returned `surf2vol: Command not found.` Prior to this, I had already set the `$SUBJECTS_DIR` environment variable and copied `/Applications/freesurfer/dev/subjects/cvs_avg35_inMNI152` to the `$SUBJECTS_DIR` directory. (1) Platform: MacBook Pro M2, macOS 15.3.2, (2) FreeSurfer version: freesurfer-macOS-darwin_arm64-dev-20240909-9ca95c6, downloaded from https://secure-web.cisco.com/13S72PTy2Rml5OEF_iEDV7rKCaavxBKyn_pl6E6oQ4EUXh… Thanks, XS

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license.txt
by Mohammed Hassan ALMorabet 07 Apr '25

07 Apr '25

External Email - Use Caution where the license.txt

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samseg: unrecognized flag with --lesion-mask-pattern
by Simone Cauzzo 07 Apr '25

07 Apr '25

External Email - Use Caution Dear support I'm running samseg using Freesurfer 7.4.0. I'm using t1, t2 and flair as input. I'm not sure if it's necessary to specify --lesion-mask-pattern but if I try, I get an unrecognized flag error as it reads the second input to --lesion-mask-pattern as a new flag. Log: ERROR: Flag 1 unrecognized. --t1w [...]/001.mgz --flair [...]/oFL.mgz --t2w [...]/oT2.mgz --s [...]01 --recon --use-flair --refmode t1w --pallidum-separate --lesion --fill --threads 16 --lesion-mask-pattern 0 1 1 if I remove the "--lesion-mask-pattern 0 1 1" I don't get any error. Any suggestion? Thanks Simone

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samseg: erroneous lesion labels on T2 red nucleus set to zero
by Simone Cauzzo 07 Apr '25

07 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? [image: Screenshot from 2025-04-02 15-20-51.png] Simone Cauzzo

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Missing data for diffusion processing tutorial
by Andrei Bieger 06 Apr '25

06 Apr '25

External Email - Use Caution Dear Freesurfer developers, I am trying to follow the Diffusion Processing Tutorial (https://secure-web.cisco.com/1ck8X8dlcraSHUFUd5cZoLiUQsXCM6JLEEH7rZnRzPLrjF…) while using tutorial data from the Freesurfer Tutorial Datasets (https://secure-web.cisco.com/1Ju0TalvW2sEV8I-BJvXQvCMSvz6QCUYH9pTC2BWw9YWxy…) After preparing the environment variables and starting Freesurfer, the next step would be dt_recon --b bvals.dat bvecs.dat --i $TUTORIAL_DIR/$subj/orig/6-1.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon The problem is, there is no …/Diff001/orig in the tutorial data, only the dtrecon folder, as you can see below: Can you help me with this? Thank you in advance, Andrei

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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

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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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