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How to use main commands⚓︎

Command Line Interface (CLI)⚓︎

How to launch dcm2bids when you have build your configuration file ? First cd in your BIDS directory.

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dcm2bids -d DICOM_DIR -p PARTICIPANT_ID -c CONFIG_FILE

If your participant have a session ID:

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dcm2bids -d DICOM_DIR -p PARTICIPANT_ID -s SESSION_ID -c CONFIG_FILE

dcm2bids creates log files inside tmp_dcm2bids/log

See dcm2bids -h or dcm2bids --help to show the help message that contains more information.

Important

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 -d "DICOM DIR" -p PARTICIPANT_ID -c "path/with spaces to/CONFIG FILE.json"

Output⚓︎

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 --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.

Tools⚓︎

  • Helper
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dcm2bids_helper -d DICOM_DIR [-o OUTPUT_DIR]

To build the configuration file, you need to have a example of the sidecars. You can use dcm2bids_helper with the DICOMs of one participant. It will launch dcm2niix and save the result inside the tmp_dcm2bids/helper of the output directory.

  • Scaffold
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dcm2bids_scaffold [-o OUTPUT_DIR]

Create basic BIDS files and directories in the output directory (by default folder where the script is launched).

  1. 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. ↩

Last update: 2023-07-24
Created: 2022-04-19