9. Manipulation brain volumes with nilearn

In this section, we detail the general tools to manipulate of brain images with nilearn.

• 9.1. Input and output: neuroimaging data representation
  • 9.1.1. Inputing data: file names or image objects
    • 9.1.1.1. File names and objects, 3D and 4D images
    • 9.1.1.2. File name matching: “globbing” and user path expansion
  • 9.1.2. Fetching open datasets from Internet
  • 9.1.3. Understanding neuroimaging data
    • 9.1.3.1. Nifti and Analyze data
    • 9.1.3.2. Niimg-like objects
    • 9.1.3.3. Text files: phenotype or behavior
• 9.2. Manipulating images: resampling, smoothing, masking, ROIs…
  • 9.2.1. Functions for data preparation and image transformation
  • 9.2.2. Resampling images
    • 9.2.2.1. Resampling one image to match another one
    • 9.2.2.2. Resampling to a specific target affine, shape, or resolution
  • 9.2.3. Accessing individual volumes in 4D images
  • 9.2.4. Computing and applying spatial masks
    • 9.2.4.1. Extracting a brain mask
    • 9.2.4.2. Masking data: from 4D Nifti images to 2D data arrays
  • 9.2.5. Image operations: creating a ROI mask manually
• 9.3. From neuroimaging volumes to data matrices: the masker objects
  • 9.3.1. The concept of “masker” objects
  • 9.3.2. NiftiMasker: applying a mask to load time-series
    • 9.3.2.1. Custom data loading: loading only the first 100 time points
    • 9.3.2.2. Controlling how the mask is computed from the data
      • 9.3.2.2.1. Visualizing the computed mask
      • 9.3.2.2.2. Different masking strategies
      • 9.3.2.2.3. Extra mask parameters: opening, cutoff…
    • 9.3.2.3. Common data preparation steps: smoothing, filtering, resampling
      • 9.3.2.3.1. Smoothing
      • 9.3.2.3.2. Temporal Filtering and confound removal
      • 9.3.2.3.3. Resampling: resizing and changing resolutions of images
    • 9.3.2.4. Inverse transform: unmasking data
  • 9.3.3. Extraction of signals from regions: NiftiLabelsMasker, NiftiMapsMasker
    • 9.3.3.1. Regions definition
    • 9.3.3.2. NiftiLabelsMasker Usage
    • 9.3.3.3. NiftiMapsMasker Usage
  • 9.3.4. Extraction of signals from regions for multiple subjects: MultiNiftiMasker, MultiNiftiLabelsMasker, MultiNiftiMapsMasker
    • 9.3.4.1. MultiNiftiMasker Usage
    • 9.3.4.2. MultiNiftiLabelsMasker Usage
    • 9.3.4.3. MultiNiftiMapsMasker Usage
  • 9.3.5. Extraction of signals from seeds: NiftiSpheresMasker
  • 9.3.6. Extraction of signals from surface images SurfaceMasker, SurfaceLabelsMasker, SurfaceMapsMasker, MultiSurfaceMasker