emorycn2l/smart_dicom_to_nifti repository overview

⁠DICOM to NIfTI Converter

The smart_dicom_to_nifti tool converts brain MRI data from DICOM format to NIfTI format and organizes the output according to the Brain Imaging Data Structure (BIDS) standard. Developed by the Computational Neuroimaging & Neuroscience Lab (CN2L), this Docker-based solution simplifies the structuring and description of neuroimaging and behavioral data.

⁠Key Features

• DICOM to NIfTI Conversion: Converts DICOM files to NIfTI format, ensuring compatibility with popular neuroimaging analysis tools.
• BIDS-Compliant Output: Produces data organized in the BIDS standard for consistency and ease of sharing.

⁠Prerequisites

• Docker installed on your system.
• Brain MRI imaging data in DICOM format.

⁠EXAMPLE Usage

1. Run the container:

   docker run -v </YOUR/PATH/TO/dicom_folder>:/input \
              -v </YOUR/PATH/TO/output_folder>:/output \
              smart_dicom_to_nifti -d /input/{subject}/{session}/*/*.dcm \
                                   -o /output -f /src/heudiconv/heuristic.py \
                                   -s "<SUBJECT ID>" -ss "<SESSION ID>" \
                                   -c dcm2niix --bids --overwrite
   
   

   Copy

⁠Flag Options

• -d DICOM_DIR_TEMPLATE | --files FILES:
  Defines the path to the DICOM files and their extension. Example:
  dicom/{subject}///*.dcm specifies that the DICOM files are located in the given path and have the .dcm extension.

• -o OUTDIR:
  Specifies the output directory for the NIfTI files. Example:
  Nifti/ is the output directory. If it does not exist, it will be created.

• -f PATH:
  Path to the heuristic.py file.

• -s SUBJECT:
  Specifies the subject number. Example: 1234567.

• -ss SESSION:
  Specifies the session ID. Example: 1.2.3456789.1223344.31423360.

• -c {dcm2niix,none}:
  Conversion option:

  • dcm2niix: Perform the conversion.
  • none: Indicates no conversion will be performed.

• -b BIDSOPTION1, BIDSOPTION2:
  Additional BIDS options.

For more flag options, consult the HeuDiConv documentation⁠.