bidspreprocess

Docker image for converting DICOMS to BIDS that supports anatomical defacing. Uses PyDeface 2.0.0 (https://github.com/poldracklab/pydeface) and dcm2bids 2.1.4 (https://github.com/cbedetti/Dcm2Bids/)

Usage of bidsconvert.py

The current docker image can be pulled from the docker hub as follows. The image takes up about 14 Gb because of the dependency of pydeface on FSL.

docker pull orbisys/bidspreprocess:0.1

Open a terminal and run docker image as shown further below to convert dicoms in $PWD/DICOM to BIDS format in $PWD/nifti using the helper python program bidsconvert.py.

This example creates bids files for subject 106 and for a session post thus creating the folder structure sub-106 -> ses-post ->

The BIDS configuration file is passed using --bidsconfig - an example of this file is available at https://cbedetti.github.io/Dcm2Bids/config/

Additionally a bids action file can also be passed using --bidsaction - this is not part of the dcm2bids ecosystem and provides a means of copying files once they have been created to other folders within the bids structure.

This functionality is under construction and provides support for copy operations only at the moment.

docker run  --rm -v $PWD:/mnt                    \ 
                  -v $PWD/DICOM:/dicom           \
                  -v $PWD/nifti:/nifti           \
                  orbisys/bidspreprocess:0.1     \   
                  python /src/bidsconvert.py     \ 
                  --subject 106 --session_label post --dicomdir /dicom --niftidir /nifti --bidsconfig /mnt/dcm2bids_config.json --bidsaction /mnt/dcm2bids_actions.json --overwrite True

Usage of dcm2bids and dcm2niix directly

Alternatively users can ignore bidsconvert.py and directly call dcm2bids or dcm2niix within the container. Simply replace bidsconvert.py in the call above with the command you prefer instead.

Example running dcm2bids help

docker run  --rm -v $PWD:/mnt                 \
                  -v $PWD/DICOM:/dicom        \
                  -v $PWD/nifti:/nifti        \
                  orbisys/bidspreprocess:0.1  \
                  dcm2bids --help

Example showing basic call to dcm2niix

docker run  --rm -v $PWD:/mnt                 \
                  -v $PWD/DICOM:/dicom        \
                  -v $PWD/nifti:/nifti        \
                  orbisys/bidspreprocess:0.1  \
                  dcm2niix

bidsaction file

The bidsaction file allows for simple copying operations using a json file format that is very similar to the dcm2bids configuration file. For example this configuration file below:

{
    "copy": [
        {
        "dataType": "func",
        "modalityLabel": "bold",
        "customLabels": "task-rest",
        "destination": {
            "modalityLabel": "sbref",
            "customLabels": "task-dummy"
            }
        },
        {
        "dataType": "anat",
        "modalityLabel": "T1w",
        "destination": {
            "modalityLabel": "FLAIR",
            "customLabels": "acq-nd"
            }
        }
		
    ]
}

Will end up copying functional files called $SUB_$SES_task-rest_bold to $SUB_$SES_task-dummy_sbref and also copying anatomical files called $SUB_$SES_T1w to $SUB_$SES_acq-nd_FLAIR where $SUB and $SES are the implied subject and session of the BIDS file.

Defacing

PyDeface (https://github.com/poldracklab/pydeface) is used to deface any anatomicals that are converted to BIDS. Currently the default output is created with the _defaced suffix. It is however also possible to call pydeface directly as follows

docker run  --rm -v $PWD:/mnt                 \
                  -v $PWD/DICOM:/dicom        \
                  -v $PWD/nifti:/nifti        \
                  orbisys/bidspreprocess:0.1  \
                  pydeface