fMRIStroke: A preprocessing pipeline for fMRI Data from Stroke patients

fMRIStroke is a functional magnetic resonance imaging (fMRI) data
quality checks and preprocessing pipeline tailored to stroke data. It is designed to provide an easily accessible,
interface that is robust to variations in scan acquisition
protocols and that requires minimal user input, while providing easily
interpretable and comprehensive reports.
It uses fmriprep outputs derivatives to generate
new quality checks plots for stroke patients when lesion masks are available and
computes new confounds like signals in lesion masks, and ICA based confounds (as proposed in [Yourganov2017]_).

The fMRIStroke pipeline uses a combination of tools from well-known software packages, including ANTs,  FreeSurfer, Rapidtide and Nilearn.

In summary this tool allows you to easily do the following:

- Generate preprocessing quality reports specific to stroke patients, with which the user can easily
  identify outliers.
- Receive verbose output concerning the stage of preprocessing for each
  subject, including meaningful errors.
- Automate and parallelize processing steps, which provides a significant
  speed-up from manual processing or shell-scripted pipelines.

Acknowledgements
----------------
This work makes great use of the work by the NiPreps Community 
and the work done by rapidtides authors.