Pipelines

Module contents

Proposed pipeline definitions for MRI data using commonplace neuroimaging analysis interfaces.

Pipeline definitions are aggregated in pipeline_definitions and may be added to the database using the Pipeline.objects.from_list() method.

Example

from django_analyses.models.pipeline import Pipeline
from django_mri.analysis.pipeline_definitions import pipeline_definitions

Pipeline.objects.from_list(pipeline_definitions)

Submodules

django_mri.analysis.pipelines.basic_fsl_preprocessing module

django_mri.analysis.pipelines.dwi_preprocessing module

Full DWI preprocessing pipeline.

Steps:

  • Extract b0 from AP
  • Merge AP_b0 and PA
  • Create brain mask
  • Convert to mif (merged, AP)
  • Denoise initial AP
  • dwifslpreproc AP merged
  • Gibbs correction
  • Bias correction

User inputs:

  • fslroi node: in_file [AP]
  • fslmerge node: in_files [PA]
  • mrconvert_1 –> AP: in_bvec [bvec]
  • mrconvert_1 –> AP: in_bval [bval]

django_mri.analysis.pipelines.fieldmap_correction module

Field-map correction for EPI scans using FSL.