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November 30, 2016 ยท View on GitHub

#+TITLE: DAC2BIDS

  • Introduction A set of utilities to automatize the conversion of DICOM into NIfTI files and to organize the output conforming to the [[http://bids.neuroimaging.io/][BIDS]] format. DAC2BIDS tries to be as compatible as possible with the Donders Institute DAC (Data Acquisition Collection).

The recommended workflow is:

  1. Generate a bids folder structure for your project. Example: #+BEGIN_SRC bash :eval never mkdir -p experiment-datasets/sub-{01,02}/ses-{01-02}/{func,anat,fmap} #+END_SRC
  2. Generate yaml files with dac2bids.py. These yaml files are used as input to:
  3. Convert DICOMs to NIfTIs with dcm2niibatch.

DAC2BIDS covers step number 2 of the workflow above. The generated yaml configuration files serve a double purpose as they document what DICOM folders are being converted to what NIfTI files.

  • Dependencies Requires Python 2.7 and the following modules: =yaml= and =dicom=.

  • Installation and Usage Use =pip= to install the required modules and simply call dac2bids from the command line. See dac2bids --help for the calling syntax.

  • Limitations

Currently only supports DICOMs from latest Siemens scanners (VD13+).