Output Files

In the specified /path/to/output/dir, there will be the following outputs:

/path/to/output/dir/
└── config
├── logs
├── work
├── .snakebids
└── .snakemake

The config folder, along with the hidden .snakebids and .snakemake folders contain a record of the code and parameters used, and paths to the inputs. The logs folder contains .txt log files from the skull_stripping and model apply rules.

Work Directory

After running the workflow, the /path/to/output/dir folder will contain a work directory. All the preprocessed nii.gz files for the mri_degad program will be in the work directory with the following structure:

work/
└── sub-{subject}
    ├── n4biascorr
    ├── degad
    ├── vasc_mask
    ├── normalize
    ├── qc
    ├── registration
    └── resample

If the --skull-strip flag is included:

work/
└── sub-{subject}
    ├── n4biascorr
    ├── degad
    ├── vasc_mask
    ├── normalize
    ├── qc
    ├── registration
    ├── resample
    └── skull_strip