PennLINC/fmriprep-fake

This is a fork repo of fmriprep-fake from @djarecka

Repository with Dockerfile for creating a Docker with "fake" fmriprep: docker build -t fmriprep_fake .

The image can be also found in DockerHub: djarecka/fmriprep_fake:0.1.0.

The image takes three positional arguments: bids_dir, output_dir and analysis_level (that has to be 'participant').

It also takes two optional named arguments: --participant-label (e.g. 'sub-111') and --bids-filter-file. bids-filter-file is used to extract sessions if available under "bold" item (e.g. {"bold": {"datatype": "func", "suffix": "bold", "session": "baseline"}}).

Example of usage and output

when run without sessions (without bids-filter-file)

docker run --rm -v <local_path_for_output>:/out_tmp djarecka/fmriprep_fake:0.1.0 inp /out_tmp participant --participant-label=sub-1

out_tmp/ 
├── dataset_description.json
├── desc-aparcaseg_dseg.tsv
├── desc-aseg_dseg.tsv
├── logs
│   ├── CITATION.bib
│   ├── CITATION.html
│   ├── CITATION.md
│   └── CITATION.tex
├── sourcedata
│   └── freesurfer
│       ├── fsaverage
│       │   └── mri
│       │       └── brain.mgz
│       └── sub-1
│           └── mri
│               └── orig.mgz
├── sub-1
│   ├── anat
│   │   └── sub-1_desc-brain_mask.nii.gz
│   ├── figures
│   │   └── sub-1_desc-sdc_bold.svg
│   ├── fmap
│   │   └── sub-1_acq-task_run-1_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
│   └── func
│       └── sub-1_task-nback_space-T1w_desc-brain_mask.nii.gz
└── sub-1.html

when run without sessions (without bids-filter-file)

docker run --rm -v <local_path_for_output>:/out_tmp -v <local_path_to_directory_with_filterfile>:/code djarecka/fmriprep_fake:0.1.0 inp /out_tmp participant --participant-label=sub-1 --bids-filter-file=/code/<filter_file>

out_tmp/
├── dataset_description.json
├── desc-aparcaseg_dseg.tsv
├── desc-aseg_dseg.tsv
├── logs
│   ├── CITATION.bib
│   ├── CITATION.html
│   ├── CITATION.md
│   └── CITATION.tex
├── sourcedata
│   └── freesurfer
│       ├── fsaverage
│       │   └── mri
│       │       └── brain.mgz
│       └── sub-1
│           └── mri
│               └── orig.mgz
├── sub-1
│   ├── figures
│   │   └── sub-1_ses-baseline_desc-sdc_bold.svg
│   └── ses-baseline
│       ├── anat
│       │   └── sub-1_ses-baseline_desc-brain_mask.nii.gz
│       ├── fmap
│       │   └── sub-1_ses-baseline_acq-task_run-1_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
│       └── func
│           └── sub-1_ses-baseline_task-nback_space-T1w_desc-brain_mask.nii.gz
└── sub-1.html