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Figure Generation

NiftyOne can generate figures and videos for BIDS datasets for QC purposes using popular Python libraries, such as nibabel, numpy, etc. Possible outputs include:

General / anatomical

  • Three view - a static image for a given volume in the three anatomical orientations (coronal, axial, sagittal)
  • Slice video - a video slicing through a single orientation for a given volume
  • Three view video - a video slicing through the 4th dimension (e.g. time) in the three anatomical orientations

Three view T1w

Diffusion

  • QSpace shells - visualization of diffusion gradients in Q-space
  • DWI per shell - video visualizing diffusion volumes by gradient strength
  • Signal per volume - 2-panel video, visualizing diffusion MRI volume with associated average signal per volume

Signal per volume dwi

Functional

  • Carpet plot - Visualization of carpet plot for functional data
  • Mean / std - Visualization of mean and standard deviations of functional data

Overlaying of multiple volumes is also possible (e.g. to visualize masks, registration, etc.)

Mean / std. dev fMRI

note

These are only some of the possible visualizations. Additional visualizations can be generated - see advanced usage for more details.