Calculates CBF values based on the PD and PW files from the BCCHR scanner (3T GE750)
You will likely want to clone this folder into some kind of Scripts folder, and then add this folder to your ~/.bashrc PATH
This script...
You may need to make CBF_quantification.py exetuable: chmod +x CBF_quantification.py
This bash script uses six arguments to calculate the CBF value in grey matter based on the grey matter mask created from the dHCP Anatomical Pipeline
You may need to make the cbf_of_grey.sh file executable: chmod +x cbf_of_grey.sh
Next, typing cbf_of_grey.sh and pressing enter should give you the instructions you need
Example run (assumes you are in the main BIDS directory):
cbf_of_grey.sh derivatives/asl/sub-AMWCER01 sub-AMWCER01/perf/sub-AMWCER01_run-01_asl.nii.gz derivatives/dhcp_anat/sub-AMWCER01/sub-AMWCER01_ses-session1_T2w_restore.nii.gz derivatives/dhcp_anat/sub-AMWCER01/sub-AMWCER01_ses-session1_brainmask_drawem.nii.gz derivatives/dhcp_anat/sub-AMWCER01/sub-AMWCER01_ses-session1_drawem_tissue_labels.nii.gz derivatives/asl/sub-AMWCER01/CBF.nii.gz