Pypeline Modules

+1 : really want it+0.5: want it-1: don't want it - SPM

1. realignment
2. coregistration
3. normalization (traditional + dartel)
4. smoothing
5. first level estimation
6. 2nd level analysis (anova, ancova, etc.,.)
7. PPI

8. fieldmap correction
9. first level analysis using surface smoothed data

- FSL
1. bet
2. flirt
3. fnirt
4. feat
5. melodic
6. fugue

7. tbss (essentially a DTI pipeline)

-  FreeSurfer

1. mri_convert (DICOM to nifti, among other things. It's really tuned to our Siemens scanners)

2. recon-all (surface extraction)
3.
bbregister (very nice program to coregister partial/full epi to
surfaces, i.e., structurals. This works better than most things I've
seen)
4. parcellation (using user defined atlases)

5. smoothing using surfaces
6. group analysis from surface data
7. motion correction using bbregister

- Misc

1. artifact detection (needs update to latest features in corresponding matlab code)
2.
rex (roi extraction tool -- needs to be converted from current matlab
code to python or for the moment just called from python)
3. connectivity toolbox