fMRI_QA
fMRI_QA tool used in Małopolskie Centrum Biotechnologii, Jagiellonian University
Tool has the following prerequisit on the fp;der structure of DICOM files. The files inside working directory should be grouped inside folders named with study date. Inside there should be a folder named fBIRN containing phantom scan data according BIRN QA suggestions: http://www.birncommunity.org/tools-catalog/function-birn-stability-phantom-qa-procedures/
How to use
Obtain docker file locally:
make pull
To see the available options run
docker run -it neuromcb/fmri_qa:latest -h
Other parameters that can be modified are stored in config.py
.
To run single analysis on default parameters, map your local drive into the docker container:
docker run -it -v "C:\Data":/data neuromcb/fmri_qa:latest -mode single -input /data/some_folder/ -output /data/some_other_folder/
To run multi analysis on default parameters:
docker run -it -v "C:\Data":/data neuromcb/fmri_qa:latest -mode single -input /data/some_folder/ -output /data/some_other_folder/
Mode description
single
mode will only generate tabular results (csv file)multi
mode will generate tabular results and graphs. The gtaphs generated in the-output
folder. To see full reports follow:output/graphs/plotly_dashboard/index.html