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Python processing for PreClinical data.

API documentation of pypreclin.workflowΒΆ

Module that provides common workflows.


pypreclin.workflow.preproc_fmri

fMRI preprocessings using FSL, SPM, JIP, and ANTS.

Steps

  1. Slice Timing correction (with cache).
  2. B0 inhomogeneties correction (optional, with cache).
  3. Reorient images not in RAS coordinate system and reorient images to match the orientation of the standard MNI152 template (with cache).
  4. Realign: motion correction - adjust for movement between slices (with cache).
  5. Normalization: warp images to fit to a standard template brain (with cache).
  6. Tissues segmentation and spatial intensity variations correction (with cache).
  7. Coregistration: overlay structural and functional images - link functional scans to anatomical scan (with cache).
  8. Wrap functional: resample the functional serie and mask the registered serie (with cache).
  9. Smooth the functional time serie (with cache).
  10. SNAPs: compute some snaps assessing the different processing steps (with cache).
  11. Reporting: generate a QC reporting (with cache).

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© 2020, Antoine Grigis Jordy Tasserie Bechir Jarraya .
Inspired by AZMIND template.