How to use main commands⚓︎
Command Line Interface (CLI)⚓︎
How to launch dcm2bids when you have build your configuration file ? First
in your BIDS directory.
If your participant have a session ID:
dcm2bids creates log files inside
dcm2bids -h or
dcm2bids --help to show the help message that contains
If your directory or file names have space in them, we recommend that you
change all the spaces for another character (
-) but if you can't
change the names, you have to wrap each argument with quotes as in the
dcm2bids -d "DICOM DIR" -p PARTICIPANT_ID -c "path/with spaces to/CONFIG FILE.json"
dcm2bids creates a
sub-<PARTICIPANT_ID> directory in the output directory (by
default the folder where the script is launched).
Sidecars with one matching description will be convert to BIDS. If a file
already exists, dcm2bids won't overwrite it. You should use the
option to overwrite files.
If a description matches several sidecars, dcm2bids will add automatically the
run- to the filename.
Sidecars with no or more than one matching descriptions are kept in
tmp_dcm2bids directory. Users can review these mismatches to change the
configuration file accordingly.
To build the configuration file, you need to have a example of the sidecars. You
dcm2bids_helper with the DICOMs of one participant. It will launch
dcm2niix and save the result inside the
tmp_dcm2bids/helper of the output
Create basic BIDS files and directories in the output directory (by default folder where the script is launched).
For each acquisition,
dcm2niixcreates an associated
.jsonfile, containing information from the dicom header. These are known as sidecars. These are the sidecars
dcm2bidsuses to filter the groups of acquisitions.