Scripting dcm to bids conversion

1

Hi all,

I am currently working on fMRI datasets of people with schizophrenia. In regard to this, I have used “dcm2niix” in MRIcroGL to convert the each of the subfolder dicom files of the participant to NIFTI format. Later used the “niix2bids” in the control panel to convert into BIDS format. Using this way, I was only able to do for one participant at a time. So, my questions are:

  1. Is there a way to do the conversion together for each participant across their sub folders?
  2. Can we write a script in the python environment for this particular conversion?

Since, I am a beginner to fMRI analysis with no proper computer science background, I would really appreciate any help provided from your side. Kindly let me know if I need to provide with more details.

Thank you!

2

Hi @Mahima,

Yes, there are several tools to do this, including dcm2bids, BIDSCoin, and Heudiconv (all of which use dcm2niix under the hood). Although, these tools may more natively be run in the terminal command line rather than python.

Best,
Steven