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Merge pull request #47 from openneuropet/46-standardize-input-names-across-pet-prep-piplines
updated to be more bids-app like
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‎README.md‎

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@@ -35,46 +35,49 @@ This software can be installed via source or via pip from PyPi with `pip install
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**_NOTE:_** This project is currently in beta release, some features listed below may not be available for version numbers < 1.0.0
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```bash
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usage: petdeface.py [-h] [--output_dir OUTPUT_DIR] [--anat_only]
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[--subject SUBJECT] [--session SESSION] [--docker]
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[--singularity] [--n_procs N_PROCS] [--skip_bids_validator]
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[--version] [--placement PLACEMENT] [--remove_existing]
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[--excludesubject] input_dir
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usage: petdeface.py [-h] [--anat_only] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--docker] [--singularity] [--n_procs N_PROCS]
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[--skip_bids_validator] [--version] [--placement PLACEMENT] [--remove_existing] [--preview_pics]
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[--participant_label_exclude participant_label_exclude [participant_label_exclude ...]] [--session_label SESSION [SESSION ...]]
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[--session_label_exclude session_label_exclude [session_label_exclude ...]]
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bids_dir [output_dir] [analysis_level]
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PetDeface
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positional arguments:
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input_dir The directory with the input dataset
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bids_dir The directory with the input dataset
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output_dir The directory where the output files should be stored, if not supplied will default to <bids_dir>/derivatives/petdeface
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analysis_level This BIDS app always operates at the participant level, if this argument is changed it will be ignored and run as a participant level
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analysis
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options:
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-h, --help show this help message and exit
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--output_dir OUTPUT_DIR, -o OUTPUT_DIR
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The directory where the output files should be stored
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--anat_only, -a Only deface anatomical images
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--subject SUBJECT, -s SUBJECT
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The label of the subject to be processed.
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--session SESSION, -ses SESSION
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The label of the session to be processed.
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--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], -pl PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
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The label(s) of the participant/subject to be processed. When specifying multiple subjects separate them with spaces.
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--docker, -d Run in docker container
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--singularity, -si Run in singularity container
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--n_procs N_PROCS Number of processors to use when running the workflow
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--skip_bids_validator
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--version, -v show programs version number and exit
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--version, -v show program's version number and exit
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--placement PLACEMENT, -p PLACEMENT
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Where to place the defaced images. Options are
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'adjacent': next to the input_dir (default) in a folder appended with _defaced
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'inplace': defaces the dataset in place, e.g. replaces faced PET and T1w images
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w/ defaced at input_dir
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'derivatives': does all of the defacing within the derivatives folder in input_dir.
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--remove_existing, -r Remove existing output files in output_dir.
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--excludesubject EXCLUDESUBJECT [EXCLUDESUBJECT ...]
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Exclude a subject(s) from the defacing workflow. e.g. --excludesubject sub-01 sub-02
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Where to place the defaced images. Options are 'adjacent': next to the bids_dir (default) in a folder appended with _defaced'inplace':
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defaces the dataset in place, e.g. replaces faced PET and T1w images w/ defaced at bids_dir'derivatives': does all of the defacing within
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the derivatives folder in bids_dir.
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--remove_existing, -r
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Remove existing output files in output_dir.
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--preview_pics Create preview pictures of defacing, defaults to false for docker
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--participant_label_exclude participant_label_exclude [participant_label_exclude ...]
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Exclude a subject(s) from the defacing workflow. e.g. --participant_label_exclude sub-01 sub-02
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--session_label SESSION [SESSION ...]
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Select only a specific session(s) to include in the defacing workflow
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--session_label_exclude session_label_exclude [session_label_exclude ...]
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Select a specific session(s) to exclude from the defacing workflow
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```
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Working example usage:
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```bash
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petdeface /inputfolder --output_dir /outputfolder --n_procs 16 --skip_bids_validator --placement adjacent
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petdeface /inputfolder /outputfolder --n_procs 16 --skip_bids_validator --placement adjacent
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```
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### Docker Usage
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-v /Data/defaced_pet_data/:/output \
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-v /home/freesurfer/license.txt:/opt/freesurfer/license.txt \
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--platform linux/amd64 \
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petdeface:latest /input --output_dir /output --n_procs 16 --skip_bids_validator --placement adjacent --user=$UID:$GID system_platform=Linux
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petdeface:latest /input /output --n_procs 16 --skip_bids_validator --placement adjacent --user=$UID:$GID system_platform=Linux
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```
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### Singularity Usage
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with `singularity exec -e`
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```bash
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singularity exec -e --bind license.txt:/opt/freesurfer/license.txt docker://openneuropet/petdeface:0.1.1 petdeface /input --output-dir /output --n_procs 10
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singularity exec -e --bind license.txt:/opt/freesurfer/license.txt docker://openneuropet/petdeface:0.1.1 petdeface /input /output --n_procs 10
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```
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**_NOTE_**: Testing with singularity has been limited to version singularity-ce 4.2.0, please let us know in the issues section of this repo if you have

‎docs/usage.rst‎

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The number of processors made available to PETdeface can be set by the `--n_procs` flag e.g.::
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petdeface /inputfolder --output_dir /outputfolder --n_procs 4
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petdeface /inputfolder /outputfolder --n_procs 4
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Additional options can be found in the help menu::
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petdeface -h
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usage: petdeface [-h] [--output_dir OUTPUT_DIR] [--anat_only] [--subject SUBJECT] [--session SESSION] [--docker] [--n_procs N_PROCS] [--skip_bids_validator] [--version]
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[--placement PLACEMENT] [--remove_existing]
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input_dir
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PetDeface
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positional arguments:
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input_dir The directory with the input dataset
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options:
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-h, --help show this help message and exit
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--output_dir OUTPUT_DIR, -o OUTPUT_DIR
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The directory where the output files should be stored
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--anat_only, -a Only deface anatomical images
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--subject SUBJECT, -s SUBJECT
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The label of the subject to be processed.
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--session SESSION, -ses SESSION
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The label of the session to be processed.
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--docker, -d Run in docker container
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--n_procs N_PROCS Number of processors to use when running the workflow
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--skip_bids_validator
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--version, -v show program's version number and exit
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--placement PLACEMENT, -p PLACEMENT
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Where to place the defaced images. Options are 'adjacent': next to the input_dir (default) in a folder appended with _defaced'inplace': defaces the dataset in place,
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e.g. replaces faced PET and T1w images w/ defaced at input_dir'derivatives': does all of the defacing within the derivatives folder in input_dir.
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--remove_existing, -r
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Remove existing output files in output_dir.
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--excludesubject EXCLUDESUBJECT [EXCLUDESUBJECT ...]
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Exclude a subject(s) from the defacing workflow. e.g. --excludesubject sub-01 sub-02
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usage: petdeface.py [-h] [--anat_only] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--docker] [--singularity] [--n_procs N_PROCS]
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[--skip_bids_validator] [--version] [--placement PLACEMENT] [--remove_existing] [--preview_pics]
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[--participant_label_exclude participant_label_exclude [participant_label_exclude ...]] [--session_label SESSION [SESSION ...]]
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[--session_label_exclude session_label_exclude [session_label_exclude ...]]
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bids_dir [output_dir] [analysis_level]
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PetDeface
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positional arguments:
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bids_dir The directory with the input dataset
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output_dir The directory where the output files should be stored, if not supplied will default to <bids_dir>/derivatives/petdeface
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analysis_level This BIDS app always operates at the participant level, if this argument is changed it will be ignored and run as a participant level
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analysis
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options:
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-h, --help show this help message and exit
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--anat_only, -a Only deface anatomical images
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--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], -pl PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
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The label(s) of the participant/subject to be processed. When specifying multiple subjects separate them with spaces.
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--docker, -d Run in docker container
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--singularity, -si Run in singularity container
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--n_procs N_PROCS Number of processors to use when running the workflow
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--skip_bids_validator
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--version, -v show program's version number and exit
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--placement PLACEMENT, -p PLACEMENT
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Where to place the defaced images. Options are 'adjacent': next to the bids_dir (default) in a folder appended with _defaced'inplace':
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defaces the dataset in place, e.g. replaces faced PET and T1w images w/ defaced at bids_dir'derivatives': does all of the defacing within
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the derivatives folder in bids_dir.
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--remove_existing, -r
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Remove existing output files in output_dir.
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--preview_pics Create preview pictures of defacing, defaults to false for docker
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--participant_label_exclude participant_label_exclude [participant_label_exclude ...]
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Exclude a subject(s) from the defacing workflow. e.g. --participant_label_exclude sub-01 sub-02
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--session_label SESSION [SESSION ...]
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Select only a specific session(s) to include in the defacing workflow
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--session_label_exclude session_label_exclude [session_label_exclude ...]
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Select a specific session(s) to exclude from the defacing workflow
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Docker Based
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------------

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