Available modules

SPM

1. Realign
2. Coregister
3. Normalize
4. Segment
5. Smooth
6. Level 1 - Model Specification
7. Level 1 - Model Estimation
8. Level 1 - Contrast Estimation
9. Level 2
   1. One Sample t-test
   2. Two Sample t-test

FSL

1. Bet
2. FAST
3. FLIRT
4. FNIRT
5. MCFLIRT

FreeSurfer

1. Dicom2Nifti - converts dicom to nifti files using mri_convert (knows a lot of siemens specific fields)
2. Recon-all
3. Resample - allows one to upsample or downsample data
4. BBregister
5. Smooth - integrated volume + surface smoothing

Misc

1. ArtifactDetection - detects outliers in functional runs based on motion and intensity.
2. IO - these are generic routines for structuring data into and out of the pipelines

1. DataSource
2. DataSink
3. DataGrabber