Finalize dependencies

[tsalo]

At minimum, I think we need:

• AFNI 3dTShift, for slice timing correction
• FSL SUSAN, to smooth BOLD data before running MELODIC
• FSL MELODIC, to perform the ICA

ICA-AROMA (https://github.com/maartenmennes/ICA-AROMA) uses the following FSL commands as well:

• bet
• fslmaths
• fslinfo
• zeropad
• fslroi
• fslmerge
• flirt
• applywarp
• fslstats
• fsl_regfilt

Of course, most, if not all, of the ICA-AROMA dependencies could be replaced with Python code. Not sure if a fork with that change already exists. I know that the ME-ICA team (myself included) worked hard to write a pure Python version, but progress on that stalled when we tried to extend ICA-AROMA to work on native-space BOLD data. Still, it might be worth resurrecting: https://github.com/ME-ICA/aroma.

Do we need any other non-Python dependencies?

[tsalo]

I had forgotten ANTs, but everything should be working now.