fMRI confound regression with conf_reg_pkg

After processing fMRI images with RABIES, the confound regression step can be accomplished with a subsequent python package https://github.com/Gab-D-G/conf_reg_pkg.
To install the software:

#go to the desired directory to install the package
git clone https://github.com/Gab-D-G/conf_reg_pkg
cd conf_reg_pkg
bash install.sh
#assuming you have RABIES installed
source activate rabies
confound_regression.py --help

The help message should show up with the instructions and options to apply a confound regression.
You have to activate the RABIES python environment and load ANTs and FSL modules to run the software:

source activate rabies
module load ANTs FSL

Example command syntax:

confound_regression.py /rabies_outputs /output_directory/diagnosis_mot24_WM_CSF_VASC_highpass0.01 \
--commonspace_bold --conf_list WM_signal CSF_signal vascular_signal mot_24 --diagnosis_output --seed_list /seeds/left_retrosplenial.nii.gz /seeds/left_somatosensory.nii.gz --highpass 0.01 \
-p Linear