gladomat / dcm2bids

Convert DICOM images to BIDS

Dcm2Bids

Dcm2Bids helps you to convert DICOM files of a study to Brain Imaging Data Structure (BIDS).

Learn more about BIDS and read the specifications.

Dcm2Bids was originally developed by Christophe Bedetti. This fork has several additional features and is maintained by Johan Carlin.

Install

git clone https://github.com/jooh/Dcm2Bids

Add the installation directory to your PYTHONPATH and the scripts directory to your PATH.

Software dependencies

• dcm2niix

DICOM to NIfTI conversion is done with dcm2niix converter. See their github for source or NITRC for compiled versions.

Usage

usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT -c CONFIG
                [-s SESSION] [--clobber] [-n SELECTSERIES [SELECTSERIES ...]]
                [-o OUTPUTDIR] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                [-a ANONYMIZER]

optional arguments:
  -h, --help            show this help message and exit
  -d DICOM_DIR [DICOM_DIR ...], --dicom_dir DICOM_DIR [DICOM_DIR ...]
                        DICOM files directory(ies). Wild cards are supported.
  -p PARTICIPANT, --participant PARTICIPANT
                        Participant number in BIDS output
  -c CONFIG, --config CONFIG
                        JSON configuration file (see example/config.json)
  -s SESSION, --session SESSION
                        Session name/number
  --clobber             Overwrite output if it exists
  -n SELECTSERIES [SELECTSERIES ...], --selectseries SELECTSERIES [SELECTSERIES ...]
                        Select subset of series numbers (integers) for
                        conversion
  -o OUTPUTDIR, --outputdir OUTPUTDIR
                        Output BIDS study directory (default current
                        directory)
  -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        Set logging level (the log file is written to
                        outputdir)
  -a ANONYMIZER, --anonymizer ANONYMIZER
                        Anonymize each anat image by passing it to this shell
                        command (e.g., pydeface.py - the call syntax must be
                        anonymizer inputfile outputfile)

Descriptions

The description field is a list of dictionnary. Each dictionnary describes one acquisition.

Output

dcm2bids creates sub-<PARTICIPANT> directories in the output directory (by default the folder where the script is launched).

Acquisitions with no or more than one fitting descriptions are kept in tmp_dcm2niix directory. Users can review these missing acquistions to change the configuration file accordingly.