PipeDream - open source neuroimaging pipelines
Installation:
git clone [email protected]:cookpa/pipedream.git
cp pipedream/config/pipedream_config_example.sh pipedream/config/pipedream_config.sh
Then edit pipedream/config/pipedream_config.sh
Call code via the .sh wrappers, eg
pipedream/dicom2series/dicom2series.sh
The code here is mostly for pre-processing, most advanced processing has been relocated to ANTs.
See
Specifically, antsCorticalThickness.sh replaces the T1 cortical thickness pipeline that was previously implemented here.
The main use of Pipedream is for data organization using GDCM (to sort data) and dcm2nii (to convert it to Nifti).