7T BIDS organiser

Tools to organise 7T data into BIDS structure

Bash and python scripts to convert DICOM data into BIDS-organised NIfTI data.

The folder structure will be

• Original dicoms in /dicomdir
• Re-named and re-arranged dicoms in are /sourcedata, which is the BIDS sourcedata-folder
• BIDS-organised NIfTIs in /rawdata

To complete the conversion:

1. Run script DcmDicomdir_to_DcmSourcedata.sh \ This re-names the dicoms and sorts them into /sourcedata

2. Run script DcmSourcedata_to_NiftiRawdata_generate_Dicominfo.sh \ Runs heudiconv without conversion Generates /rawdata/.heudiconv/sub-$sID/dicominfo.tsv which is used to generate a relevant heuristic file for input to heudiconv.

3. Run script DcmSourcedata_to_NiftiRawdata.sh \ This converts the dicoms in /sourcedata to BIDS-organised NIfTIs in /rawdata using the heudiconv routine.

   • heudiconv is run with using a Docker container using rules set in the python file 7T049_CVI_heuristic.py
   • The script also makes a BIDS-validation

4. Run script MRIQC.sh \ This script runs MRIQC on the data