This script was created for converting Siemens-outputted DICOM files (in which the folder structure is as follows: "Project / Session Folder" > "MR Sequence Folder" > "DICOM folder") into NIFTI files. The code iterates through all MR sequence / run folders within the project / session folder, creates a new folder ("NIFTI") for dcm2niix output, then runs the dcm2niix program if there are no nifti files in this subfolder.
NOTE: You will need dcm2niix (https://github.com/rordenlab/dcm2niix/releases) installed on the device you are running this script from, and dcm2niix MUST be executable and added to your PATH. Once you install dcm2niix (it will come to you as a shell file), move the file into a folder called dcm2niix_folder. In Terminal, go to this folder and enter the following line of code
<chmod u+x dcm2niix>
Navigate to your bash profile (this will be a text file that is located under your user folder on your device - on Mac, you can press the "Shift"-"Command"-"." keys simultaneously to reveal this in Finder) and add the following lines to the very end of this file (replace tb3344 with your own user folder name)
PATH="/Users/tb3344/Desktop/dcm2niix_folder:${PATH}"
export PATH
NOTE: if you do not already have a .bash_profile text file within your user folder, you can create one in Terminal by entering the following code
cd ~
touch .bash_profile
Run this script within the MRI session folder (e.g. R21_EEG-fMRI_001_v2) in Terminal by calling
<bash ~/folder-where-you-have-this-script-downloaded/NIFTIconversion.sh>