This a BIDS App wrapper for Pydeface. Like every BIDS App it consists of a container that includes all of the dependencies and run script that parses a BIDS dataset. BIDS Apps run on Windows, Linux, Mac as well as HCPs/clusters.
Pydeface BIDS App will grab the images corresponding to the subject and image modality requested and run Pydeface on them, overwritting the original images.
Please read the official Pydeface docs.
Experiencing problems? Please open an issue and explain what's happening so we can help.
This App has the following command line arguments:
usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[--session_label SESSION_LABEL [SESSION_LABEL ...]]
bids_dir output_dir {participant}
Pydeface BIDS App.
positional arguments:
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
output_dir This argument is here for BIDS-Apps
compatibility. All images will be written to the bids_dir
overwriting the input.
{participant} Level of the analysis that will be performed. Multiple
participant level analyses can be run independently
(in parallel).
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be
analyzed. The label corresponds to
sub-<participant_label> from the BIDS spec (so it does
not include "sub-"). If this parameter is not provided
all subjects will be analyzed. Multiple participants
can be specified with a space separated list.
--session_label SESSION_LABEL [SESSION_LABEL ...]
The label of the session that should be analyzed. The
label corresponds to ses-<session_label> from the BIDS
spec (so it does not include "ses-"). If this
parameter is not provided all sessions should be
analyzed.
--modality MODALITY1 [MODALITY2 ...]
The modalities of images that will be defaced. They can be
either suffixes (e.g.: T1w, T2w, bold) or datatype (e.g.:
anat, func, fmap). Default: anat
--skip_bids_validator
If set, it will not run the BIDS validator before defacing.
To run it in participant level mode (for one participant):
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset \
cbinyu/pydeface \
/bids_dataset /bids_dataset participant --participant_label 01
To run it for a specific modality of images:
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset \
cbinyu/pydeface \
/bids_dataset /bids_dataset participant --participant_label 01 --modalities T1w