Proposed Interfaces - OUTDATED
Below is a brief list of interfaces we plan to implement. This
document should be temporary and eventually go into the documentation.
List of interfaces
SPM
- realignment
- realign (estimate, or estimate_write)
- realign_unwarp
- coregistration
- coregister(estimate, estimate_write)
- reslice
- (via coreg or realign)
normalization (traditional + dartel)
smoothing
first level estimation
2nd level analysis (1sample-ttest, 2sample-ttest, anova,
correlations, etc.,.) - satra
PPI
fieldmap correction
first level analysis using surface smoothed data
DCM
FSL
- bet
- flirt
- fnirt
- feat
- melodic
- fugue
- tbss (essentially a DTI pipeline)
- first
- possum
FreeSurfer
- mri_convert (DICOM to nifti, among other things. It’s really tuned
to our Siemens scanners)
- recon-all (surface extraction)
- bbregister (very nice program to coregister partial/full epi to
surfaces, i.e., structurals. This works better than most things
I’ve seen)
- parcellation
- smoothing using surfaces
- group analysis from surface data
- motion correction using bbregister
- atlas training
- template creation
Afni
- to3d
- 3drefit
- 3dresample
- 3dTstat
- 3dAutomask
- 3dvolreg
- 3dmerge
- 3dZcutup
- 3dSkullStrip