Comments (4)
Maybe this did not copy correctly, but after the user flag you should put: --user $(id -u):$(id -g)
also, because of the latest tag, we cannot see from this which version you are really running. It will not download the latest version if that tag already exists locally. It is safer to use (currently): deepmi/fastsurfer:gpu-v2.2.0
although probably that is the same version.
And can you post the full output? Is the only ERROR "Flag unrecognised"?
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(base) user1nrx@srv-imgrm-04:~/software_research/my_fastsurfer_analysis$ sudo docker run --gpus all -v /home/user1nrx/software_research/my_fastsurfer_analysis/data:/data -v /home/user1nrx/software_research/my_fastsurfer_analysis/output:/output -v /home/user1nrx/software_research/my_fastsurfer_analysis/freesurfer_license:/fs_license --entrypoint "/fastsurfer/brun_fastsurfer.sh" --rm --user
/fastsurfer/brun_fastsurfer.sh --fs_license /fs_license/license.txt --sd /output --subject_list /data/subject_list.txt --parallel –threads 16 --3T --debug
Fri, 14 Jun 2024 09:21:20 +0000
---START DEBUG---
Debug parameters to script brun_fastsurfer:
subjects:
subject1=/data/sub-01/sub-01_T1w.nii subject2=/data/sub-02/sub-02_T1w.nii subject3=/data/sub-03/sub-03_T1w.nii subject4=/data/sub-04/sub-04_T1w.nii
task_id/task_count: /
running default
FastSurfer parameters:
--fs_license /fs_license/license.txt
--sd /output
--parallel –threads 16
--3T
Running in /usr/bin/bash
---END DEBUG ---
INFO: run_fastsurfer not explicitly specified, using $FASTSURFER_HOME/run_fastsurfer.sh.
DEBUG: subject 1: subject1=/data/sub-01/sub-01_T1w.nii
DEBUG: /fastsurfer/run_fastsurfer.sh --sid subject1 --t1 /data/sub-01/sub-01_T1w.nii --fs_license /fs_license/license.txt --sd /output --parallel –threads 16 --3T [&]
ERROR: Flag unrecognized.
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Does threads have only one "-" ? should be --threads 16
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No, its a copy paste problem. I used --threads.
But, I saw the same problem in issue #438, created by some else here, and I followed the solution that you suggested "using --seg_only and --surf_only".
It is working now.
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Related Issues (20)
- srun_fastsurfer.sh on HPC, surface pipeline fails for hundreds but works for tens of subjects HOT 8
- Question about content of wmparc.DKTatlas.mapped.mgz HOT 1
- Support for lesion masks? HOT 1
- Unmatched ROIs in predicted segmentation and provided FastSurfer_ColorLUT.tsv HOT 23
- FastSurfer Segmentation Modules: disable conformation of input image to isometric spaces HOT 5
- FastSurfer QuickSeg doesn't work with OASIS `.img` files HOT 3
- Docker build workflows HOT 5
- Model download issue HOT 22
- invalid index in smooth_aparc.py HOT 7
- DKTAtlas instead of aparc.stats file in FastSurfer HOT 3
- recon_surf//functions.sh: line 38: -debug: command not found HOT 6
- no-cache argument for build.py HOT 2
- Updated Docker Image HOT 1
- Website hosting checkpoints down HOT 5
- Anterior/Posterior Commissure Segmentation HOT 6
- ERROR: FastSurfer asegdkt segmentation failed. HOT 8
- Surface module fail in dev HOT 6
- Reference to deprecated docker images in surface pipeline docs HOT 5
- Corresponding Stats output of FastSurfer to "Recon-all" HOT 6
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