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Deep-MI / FastSurfer

PyTorch implementation of FastSurferCNN
Apache License 2.0
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Wrapper script for run_fastsurfer.sh #520

Closed zainthecoder closed 3 weeks ago

zainthecoder commented 4 months ago

This pull request introduces changes for following points:

Input File Verification:
    Ensure that all necessary input files and directories exist before launching FastSurfer. This includes:
        subject_dir
        output_dir
        FS_LICENSE
        home_dir

Container Runtime Detection:
    Determine whether Docker or Singularity is installed on the system.
    If Singularity is installed and the image is available, run FastSurfer using Singularity.
    If Singularity is not available, fall back to using Docker.

Output Directory Management:
    Check if the output directory already contains FastSurfer files.
    Implement handling for cases where files may be overwritten.

Background Execution:
    Enable FastSurfer to run in the background to allow for other processes to be executed concurrently.

Sample Command ./run_fastsurfer_wrapper.sh -b -sd /FastSurfer/my_mri_data -o /FastSurfer/my_fastsurfer_analysis --fs_license /FastSurfer/my_fs_license_dir -hd /FastSurfer