Convert DICOM files to NIFTI files

This recipe provides code for converting DICOM (.dcm) files to NIFTI (.nii) files

dcm2niix

• This recipe converts dicom to nifti files using the program dcm2niix
• https://github.com/rordenlab/dcm2niix
• The only required argument for dcm2niix is the location of the folder with the DICOM files to convert, which is always the final argument provided.

# install dcm2niix (for mac)
curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_mac.zip

# convert dicom files found in dicomdir, output to outdir
dcm2niix -o ~/outdir ~/dicomdir

dcm2niibatch (batch conversions)

• https://github.com/rordenlab/dcm2niix/blob/master/BATCH.md
• Use dcm2niibatch to perform batch conversion of multiple dicoms using the configurations specified in a yaml file
• See github link above for yaml file format

dcm2niibatch batch_config.yml

dcm2niix_afni (AFNI)

• This recipe will use afni's dcm2niix_afni to convert dicom files found in ~/dicomdir to nifti files, and output converted files into ~/outputdir
• For additional examples and options, see: https://afni.nimh.nih.gov/pub/dist/doc/program_help/dcm2niix_afni.html

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#!/bin/bash 
dcm2niix_afni -o ~/outputdir ~/dicomdir

dicom2nifti (python)

• This recipe will use the python library dicom2nifti to convert dicom files to nifti files
• https://github.com/icometrix/dicom2nifti

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# install using pip
pip install dicom2nifti

# Run
import dicom2nifti

# run from commandline:
dicom2nifti /dicom_directory /output_directory

# run from python: 
dicom2nifti.convert_directory(dicom_directory, output_directory, compression=True, reorient=True)

Recipe made by Bari Fuchs