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DICOM → NIfTI (non-BIDS)

Shared with the CNT

This procedure runs on infrastructure the lab and the CNT operate together. The CNT manual keeps its own copy; changes to the shared steps are agreed with the CNT.

What this page tells you

In cnt1 go to /project/imaging_process/programs/run_dcm2niix, unzip the dicoms (unzip '*.zip'), edit the batch script or txt file with input/output paths, and run bash dcm2niix_directory.sh; niftis appear in the output folder.

This conversion runs on cnt1 from the VDI.

  • ssh cnt1
  • cd /project/imaging_process/programs/run_dcm2niix
  • Here you can use either batch_processing or directory_processing.
    • directory_processing goes into the sub-directories within the main directory.
    • batch_processing goes into all files within the directory.

The DICOMs must be unzipped before conversion. Go to the folder and type unzip '*.zip'. All files will unzip.

For directory_processing:

  • Edit the dcm2niix_batch.sh text file with the input and output path.
  • Edit the txt file with the input and output path.

To run the code: bash dcm2niix_directory.sh

The NIfTIs will show up in the nifti output folder.