Output Files

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

/path/to/output/dir/
└── config
├── logs
├── sub-{subject}
├── 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.

Work Directory

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

For a T1w image:

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

For a T2w, FLAIR, or ct image:

work/
└── sub-{subject}
    ├── SynthSR
    ├── normalize
    ├── registration
    └── resample

When the –stereotaxy flag is specified, the ACPC tranforms are slso saved in the work directory:

work/
└── sub-{subject}
    └── ACPCtransforms
        └──*ACPC.txt

sub-{subject} directory

In the sub-{subject} directory an fcsv with the 32 anatomical fiducial locations is produced in the afids-cnn directory. When the –stereotaxy flag is used, an additional stereotaxy directory is produced with the stereotactic target locations for native space and mcp in fcsv files created. When the –fidqc flag is used, and additional fidqc directory is created with a *afids.html landmark qc file.

sub-{subject}/
    ├── afids-cnn
    ├── fidqc
    └── stereotaxy