pipedream

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

http://stnava.github.io/ANTs/

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).