User guide: table of contents

• 1. Introduction: fmralign in a nutshell
  • 1.1. Functional alignment: handling functional variability
  • 1.2. Installing fmralign
• 2. Functional alignment: handling functional variability
  • 2.1. An introduction to functional alignment
    • 2.1.1. Inter subject variability in fMRI
      • 2.1.1.1. Loading and preparing the data
      • 2.1.1.2. Measure correlation between subjects images
    • 2.1.2. Functional alignment
      • 2.1.2.1. Learning the transformation and predicting new data
      • 2.1.2.2. Measuring similarity after alignment
  • 2.2. Functional alignment pipeline
    • 2.2.1. Local functional alignment
    • 2.2.2. Alignment methods on a region
      • 2.2.2.1. Orthogonal alignment (Procrustes)
      • 2.2.2.2. Ridge alignment
      • 2.2.2.3. Optimal Transport alignment
    • 2.2.3. Comparing those methods on a region of interest
      • 2.2.3.1. Loading the data
      • 2.2.3.2. Extract a mask for the visual cortex from Yeo Atlas
      • 2.2.3.3. Define a masker
      • 2.2.3.4. Prepare the data
      • 2.2.3.5. Define the estimators, fit them and do a prediction
• 3. Reference documentation: all fmralign functions
  • 3.1. fmralign.pairwise_alignment: Pairwise Alignment
    • 3.1.1. fmralign.pairwise_alignment.PairwiseAlignment
      • PairwiseAlignment
        • PairwiseAlignment.__init__()
        • PairwiseAlignment.fit()
        • PairwiseAlignment.fit_transform()
        • PairwiseAlignment.transform()
  • 3.2. fmralign.template_alignment: Template Alignment
    • 3.2.1. fmralign.template_alignment.TemplateAlignment
      • TemplateAlignment
        • TemplateAlignment.__init__()
        • TemplateAlignment.fit()
        • TemplateAlignment.fit_transform()
        • TemplateAlignment.set_fit_request()
        • TemplateAlignment.set_transform_request()
        • TemplateAlignment.transform()
  • 3.3. fmralign.alignment_methods: Alignment Methods
    • 3.3.1. fmralign.alignment_methods.Identity
      • Identity
        • Identity.__init__()
        • Identity.transform()
    • 3.3.2. fmralign.alignment_methods.DiagonalAlignment
      • DiagonalAlignment
        • DiagonalAlignment.__init__()
        • DiagonalAlignment.fit()
        • DiagonalAlignment.transform()
    • 3.3.3. fmralign.alignment_methods.ScaledOrthogonalAlignment
      • ScaledOrthogonalAlignment
        • ScaledOrthogonalAlignment.__init__()
        • ScaledOrthogonalAlignment.fit()
        • ScaledOrthogonalAlignment.transform()
    • 3.3.4. fmralign.alignment_methods.RidgeAlignment
      • RidgeAlignment
        • RidgeAlignment.__init__()
        • RidgeAlignment.fit()
        • RidgeAlignment.transform()
    • 3.3.5. fmralign.alignment_methods.Hungarian
      • Hungarian
        • Hungarian.__init__()
        • Hungarian.fit()
        • Hungarian.transform()
    • 3.3.6. fmralign.alignment_methods.OptimalTransportAlignment
      • OptimalTransportAlignment
        • OptimalTransportAlignment.__init__()
        • OptimalTransportAlignment.fit()
        • OptimalTransportAlignment.transform()