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updated to be more bids-app like #47

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Nov 20, 2024
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updated to be more bids-app like #47

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22f3daf
updated to be more bids-app like
bendhouseart Nov 14, 2024
75e29f1
enabled anat only, cleaned up comments
bendhouseart Nov 15, 2024
5a4e1a6
added session inclusion/exclusion
bendhouseart Nov 15, 2024
6e00396
format with black
bendhouseart Nov 15, 2024
83f337c
refactored args naming
bendhouseart Nov 18, 2024
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51 changes: 27 additions & 24 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -35,46 +35,49 @@ This software can be installed via source or via pip from PyPi with `pip install
**_NOTE:_** This project is currently in beta release, some features listed below may not be available for version numbers < 1.0.0

```bash
usage: petdeface.py [-h] [--output_dir OUTPUT_DIR] [--anat_only]
[--subject SUBJECT] [--session SESSION] [--docker]
[--singularity] [--n_procs N_PROCS] [--skip_bids_validator]
[--version] [--placement PLACEMENT] [--remove_existing]
[--excludesubject] input_dir
usage: petdeface.py [-h] [--anat_only] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--docker] [--singularity] [--n_procs N_PROCS]
[--skip_bids_validator] [--version] [--placement PLACEMENT] [--remove_existing] [--preview_pics]
[--participant_label_exclude participant_label_exclude [participant_label_exclude ...]] [--session_label SESSION [SESSION ...]]
[--session_label_exclude session_label_exclude [session_label_exclude ...]]
bids_dir [output_dir] [analysis_level]

PetDeface

positional arguments:
input_dir The directory with the input dataset
bids_dir The directory with the input dataset
output_dir The directory where the output files should be stored, if not supplied will default to <bids_dir>/derivatives/petdeface
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
analysis

options:
-h, --help show this help message and exit
--output_dir OUTPUT_DIR, -o OUTPUT_DIR
The directory where the output files should be stored
--anat_only, -a Only deface anatomical images
--subject SUBJECT, -s SUBJECT
The label of the subject to be processed.
--session SESSION, -ses SESSION
The label of the session to be processed.
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], -pl PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant/subject to be processed. When specifying multiple subjects separate them with spaces.
--docker, -d Run in docker container
--singularity, -si Run in singularity container
--n_procs N_PROCS Number of processors to use when running the workflow
--skip_bids_validator
--version, -v show programs version number and exit
--version, -v show program's version number and exit
--placement PLACEMENT, -p PLACEMENT
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, 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.
--remove_existing, -r Remove existing output files in output_dir.
--excludesubject EXCLUDESUBJECT [EXCLUDESUBJECT ...]
Exclude a subject(s) from the defacing workflow. e.g. --excludesubject sub-01 sub-02
Where to place the defaced images. Options are 'adjacent': next to the bids_dir (default) in a folder appended with _defaced'inplace':
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
the derivatives folder in bids_dir.
--remove_existing, -r
Remove existing output files in output_dir.
--preview_pics Create preview pictures of defacing, defaults to false for docker
--participant_label_exclude participant_label_exclude [participant_label_exclude ...]
Exclude a subject(s) from the defacing workflow. e.g. --participant_label_exclude sub-01 sub-02
--session_label SESSION [SESSION ...]
Select only a specific session(s) to include in the defacing workflow
--session_label_exclude session_label_exclude [session_label_exclude ...]
Select a specific session(s) to exclude from the defacing workflow
```

Working example usage:

```bash
petdeface /inputfolder --output_dir /outputfolder --n_procs 16 --skip_bids_validator --placement adjacent
petdeface /inputfolder /outputfolder --n_procs 16 --skip_bids_validator --placement adjacent
```

### Docker Usage
Expand Down Expand Up @@ -107,7 +110,7 @@ docker run --user=$UID:$GID -a stderr -a stdout --rm \
-v /Data/defaced_pet_data/:/output \
-v /home/freesurfer/license.txt:/opt/freesurfer/license.txt \
--platform linux/amd64 \
petdeface:latest /input --output_dir /output --n_procs 16 --skip_bids_validator --placement adjacent --user=$UID:$GID system_platform=Linux
petdeface:latest /input /output --n_procs 16 --skip_bids_validator --placement adjacent --user=$UID:$GID system_platform=Linux
```

### Singularity Usage
Expand All @@ -127,7 +130,7 @@ Otherwise, one can run and execute petdeface with the same syntax as calling it
with `singularity exec -e`

```bash
singularity exec -e --bind license.txt:/opt/freesurfer/license.txt docker://openneuropet/petdeface:0.1.1 petdeface /input --output-dir /output --n_procs 10
singularity exec -e --bind license.txt:/opt/freesurfer/license.txt docker://openneuropet/petdeface:0.1.1 petdeface /input /output --n_procs 10
```

**_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
Expand Down
68 changes: 38 additions & 30 deletions docs/usage.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -81,40 +81,48 @@ When viewed, a succesfully defaced PET image will have varying intensities in th

The number of processors made available to PETdeface can be set by the `--n_procs` flag e.g.::

petdeface /inputfolder --output_dir /outputfolder --n_procs 4
petdeface /inputfolder /outputfolder --n_procs 4

Additional options can be found in the help menu::

petdeface -h
usage: petdeface [-h] [--output_dir OUTPUT_DIR] [--anat_only] [--subject SUBJECT] [--session SESSION] [--docker] [--n_procs N_PROCS] [--skip_bids_validator] [--version]
[--placement PLACEMENT] [--remove_existing]
input_dir

PetDeface

positional arguments:
input_dir The directory with the input dataset

options:
-h, --help show this help message and exit
--output_dir OUTPUT_DIR, -o OUTPUT_DIR
The directory where the output files should be stored
--anat_only, -a Only deface anatomical images
--subject SUBJECT, -s SUBJECT
The label of the subject to be processed.
--session SESSION, -ses SESSION
The label of the session to be processed.
--docker, -d Run in docker container
--n_procs N_PROCS Number of processors to use when running the workflow
--skip_bids_validator
--version, -v show program's version number and exit
--placement PLACEMENT, -p PLACEMENT
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,
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.
--remove_existing, -r
Remove existing output files in output_dir.
--excludesubject EXCLUDESUBJECT [EXCLUDESUBJECT ...]
Exclude a subject(s) from the defacing workflow. e.g. --excludesubject sub-01 sub-02
usage: petdeface.py [-h] [--anat_only] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--docker] [--singularity] [--n_procs N_PROCS]
[--skip_bids_validator] [--version] [--placement PLACEMENT] [--remove_existing] [--preview_pics]
[--participant_label_exclude participant_label_exclude [participant_label_exclude ...]] [--session_label SESSION [SESSION ...]]
[--session_label_exclude session_label_exclude [session_label_exclude ...]]
bids_dir [output_dir] [analysis_level]

PetDeface

positional arguments:
bids_dir The directory with the input dataset
output_dir The directory where the output files should be stored, if not supplied will default to <bids_dir>/derivatives/petdeface
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
analysis

options:
-h, --help show this help message and exit
--anat_only, -a Only deface anatomical images
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], -pl PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant/subject to be processed. When specifying multiple subjects separate them with spaces.
--docker, -d Run in docker container
--singularity, -si Run in singularity container
--n_procs N_PROCS Number of processors to use when running the workflow
--skip_bids_validator
--version, -v show program's version number and exit
--placement PLACEMENT, -p PLACEMENT
Where to place the defaced images. Options are 'adjacent': next to the bids_dir (default) in a folder appended with _defaced'inplace':
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
the derivatives folder in bids_dir.
--remove_existing, -r
Remove existing output files in output_dir.
--preview_pics Create preview pictures of defacing, defaults to false for docker
--participant_label_exclude participant_label_exclude [participant_label_exclude ...]
Exclude a subject(s) from the defacing workflow. e.g. --participant_label_exclude sub-01 sub-02
--session_label SESSION [SESSION ...]
Select only a specific session(s) to include in the defacing workflow
--session_label_exclude session_label_exclude [session_label_exclude ...]
Select a specific session(s) to exclude from the defacing workflow

Docker Based
------------
Expand Down
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