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.