Welcome to Phantom_check’s documentation!

Phantom_check is a Python library for converting U24 MRI dicoms to BIDS format and running quick quality check (QC) pipelines.

1. Copy and clean up the dicoms according to unique series number and names

2. Convert dicoms to BIDS nifti using heudiconv

3. Quick QC pipeline

   • Compares series information to another template BIDS datasource.

   • MRIQC

   • FMRIPREP

     • Freesurfer

   • Quick diffusion preprecssing

     • Topup

     • Eddy

     • eddy_squeeze

     • MKCurve

Check out the Installation and Usage section for further information.

Note

This project is under active development.

Contents

• Installation
  • Install dcm2niix
  • Install heudiconv
  • Install phantom_check
• Usage
  • dicom_to_dpacc_bids.py
  • Available options
  • Output structure
• Steps in detail
  • What the script is doing
    • 1. Sort dicom files according to series description
    • 2. Dicom to BIDS using heudiconv
    • 3. Quick quality check (QC) outputs
• Quick Quality Check
  • List of QQC outputs
    • Comparison to the standard BIDS session given by user
    • Consistency across the series in the same scan session
    • Quick summary of signals in DWI and REST fMRI
    • Quick capture of all nifti files