Practice: dcm2niix
Introduction
Goals To give you experience with dcm2niix. The dcm2niix program is the engine behind most converters that ingest DICOM data and produce the NIfTI and JSON pairs needed for BIDS. dcm2niix is available for Windows, Mac, and Linux. You should have a copy of this program for one-off conversion and troubleshooting!
Learning Objectives This lesson contributes to the objective to "explain the implementation of the BIDS standard" by providing you with experience "manipulating data with dcm2niix"
Setup
⛅️ Google Cloud Shell Tutorial
✅ Open Google Cloud Shell, and copy and paste the following command into the terminal window to download the tutorial
wget https://bitbucket.org/dpat/neuro4rii/raw/main/cloudshell_lessons/tutorial_dcm2niix.md
✅ Type teachme tutorial_dcm2niix.md to start the tutorial.
In the dcm2niix tutorial you'll download the dcm2niix tool to your bin directory and you'll download sample data to convert.
Answer the questions from the tutorial below.
Practice and Questions
Summary
Most importantly, this practice introduced you to the engine that powers most DICOM to BIDS converters. It is a good idea to have a copy of dcm2niix for one-off conversions and testing.
Less critically, you learned to use particular option flags in the dcm2niix command line.
