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Planning - OUTDATED

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Use Cases

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Proposed Interfaces - OUTDATED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

  1. realignment
    1. realign (estimate, or estimate_write)
    2. realign_unwarp
  2. coregistration
    1. coregister(estimate, estimate_write)
  3. reslice
    1. (via coreg or realign)
  4. normalization (traditional + dartel)

  5. smoothing

  6. first level estimation

  7. 2nd level analysis (1sample-ttest, 2sample-ttest, anova, correlations, etc.,.) - satra

  8. PPI

  9. fieldmap correction

  10. first level analysis using surface smoothed data

  11. DCM

FSL

  1. bet
  2. flirt
  3. fnirt
  4. feat
  5. melodic
  6. fugue
  7. tbss (essentially a DTI pipeline)
  8. first
  9. possum

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
  5. smoothing using surfaces
  6. group analysis from surface data
  7. motion correction using bbregister
  8. atlas training
  9. template creation

Afni

  1. to3d
  2. 3drefit
  3. 3dresample
  4. 3dTstat
  5. 3dAutomask
  6. 3dvolreg
  7. 3dmerge
  8. 3dZcutup
  9. 3dSkullStrip