data2bids.py - Aaronearlerichardson/CMRIF_preprocess GitHub Wiki

usage: data2bids.py [-h] [-i INPUT_DIR] [-c CONFIG] [-o OUTPUT_DIR] [-d DICOM_PATH] [-m [MULTI_ECHO [MULTI_ECHO ...]]] [-verb]

Data2bids is a script based on the SIMEXP lab script to convert nifti MRI files into BIDS format. This script has been modified to also parse README data as well as include conversion of DICOM files to nifti. The script utilizes Chris Rorden's Dcm2niix program for actual conversion.

This script takes one of two formats for conversion. The first is a series of DICOM files in sequence with an optional "medata" folder which contains any number of single or multi-echo uncompressed nifti files (.nii). Note that nifti files in this case must also have a corresponding DICOM scan run, but not necessarily scan echo (for example, one DICOM scan for run 5 but three nifti files which are echoes 1, 2, and 3 of run 5). The other format is a series of nifti files and a README.txt file formatted the same way as it is in the example. Both formats are shown in the examples folder.

Both formats use a .json config file that maps either DICOM tags or text within the nifti file name to BIDS metadata. The syntax and formatting of this .json file can be found here https://github.com/SIMEXP/Data2Bids#heuristic .

The only thing this script does not account for is event files. If you have the 1D files that's taken care of, but chances are you have some other format. If this is the case, I recommend https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/05-task-events.html so that you can make BIDS compliant event files.

Data2bids documentation at https://github.com/SIMEXP/Data2Bids Dcm2niix documentation at https://github.com/rordenlab/dcm2niix

Arguments:

  -h, --help            show this help message and exit
  -i INPUT_DIR, --input_dir INPUT_DIR
                        Input data directory(ies), must include a readme.txt
                        file formatted like example under examples folder.
                        Mutually exclusive with DICOM directory option.
                        Default: current directory
  -c CONFIG, --config CONFIG
                        JSON configuration file (see https://github.com/SIMEXP
                        /Data2Bids/blob/master/example/config.json)
  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
                        Output BIDS directory, Default: Inside current
                        directory
  -d DICOM_PATH, --DICOM_path DICOM_PATH
                        Optional DICOM directory, Mutually exclusive with
                        input directory option
  -m [MULTI_ECHO [MULTI_ECHO ...]], --multi_echo [MULTI_ECHO [MULTI_ECHO ...]]
                        indicator of multi-echo dataset. Only necessary if NOT
                        converting DICOMs. For example, if runs 3-6 were all
                        multi-echo then the flag should look like: -m 3 4 5 6
                        . Additionally, the -m flag may be called by itself if
                        you wish to let data2bids auto-detect multi echo data,
                        but it will not be able to tell you if there is a
                        mistake.
  -verb, --verbose      verbosity