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