If your directory or file names have space in them, we recommend that you
change all the spaces for another character (_ or -) but if you can't
change the names, you have to wrap each argument with quotes as in the
example below:
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 converted to BIDS. If a file
already exists, dcm2bids won't overwrite it. You should use the --clobber
option to overwrite files.
If a description matches several sidecars, dcm2bids will add automatically the
custom label 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.
the dcm2bids_scaffold command creates basic BIDS files and directories based on the bids-starter-kit. The output directory is set to the location where the script is launched by default.
To build the configuration file, you need to have examples of sidecar files. You
can use dcm2bids_helper with the DICOMs of one participant. It will launch
dcm2niix and save the result inside the tmp_dcm2bids/helper directory by default.
For each acquisition, dcm2niix creates an associated .json file,
containing information from the dicom header. These are known as
sidecars. These are the sidecars dcm2bids uses to filter the groups of
acquisitions.
To define this filtering you will probably need to review these sidecars.
You can generate all the sidecars for an individual participant using
dcm2bids_helper. ↩