...If you are looking for data organization and pre-processing code, please see the new version of PipeDream on GitHub:
https://github.com/cookpa/pipedream
It is still very much a work in progress but has dicom2series, dicom2nii, nii2dt.
If you are looking for a T1 processing pipeline, please see antsCorticalThickness.sh in the latest version of ANTs:
https://github.com/stnava/ANTs
The old PipeDream "antsbrainprocessing.sh" was a protoyype for antsCorticalThickness.sh.