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Table Of Contents

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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
  6. FSLSmooth
  7. Level1Design
  8. FSFL1Maker

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
  6. SurfConcat - projects and concatenates con images to a surface for a second level surface-based glm
  7. OneSampleTTest - surface based glm for second level analysis

Misc

  1. ArtifactDetection - detects outliers in functional runs based on motion and intensity.
  2. StimulusCorrelation - detects if stimulus schedule is correlated with motion or intensity
  3. IO - these are generic routines for structuring data into and out of the pipelines
  1. DataSource
  2. DataSink
  3. DataGrabber