SCAN-NRAD / qMriMaps

qMriMaps

About qMriMaps

Scripts related to the corresponding publication:

Köstner, M, Rebsamen, M, Radojewski, P, Rummel, C, Jin, B, Meier, R, Ahmadli, U, Schindler, K and Wiest, R.
Large-scale transient peri-ictal perfusion magnetic resonance imaging abnormalities detected by quantitative image analysis.
Brain Communications. 2023. https://doi.org/10.1093/braincomms/fcad047

Installation

Install DL+DiReCT

Follow the install instructions from https://github.com/SCAN-NRAD/DL-DiReCT

Install qMriMaps

cd ${HOME}
git clone https://github.com/SCAN-NRAD/qMriMaps.git
cd qMriMaps
pip install -e .

Install R packages

Install R >= 3.6 and make sure you have installed the following packages:

install.packages(c('remotes', 'dplyr', 'ggpubr', 'reshape2', 'grid', 'scales', 'ggrepel', 'stringr'))
remotes::install_github("LCBC-UiO/ggseg", build_vignettes = FALSE)

Usage

Prepare data

Put data in a directory structure as follows:

- data
	- subj1
		- anat
			- T1.nii.gz
		- perf
			- rBF.nii.gz
			- rBV.nii.gz
			- tMIP.nii.gz
	- subj2
		- anat
			- T1.nii.gz
		- perf
			- rBF.nii.gz
			- rBV.nii.gz
			- tMIP.nii.gz
	- ...

Run qmrimaps with:

source activate DL_DiReCT
qmrimaps data results