dmriprep package

Subpackages

• dmriprep.interfaces package
  • Submodules
  • dmriprep.interfaces.fmap module
  • dmriprep.interfaces.reportlets module
  • Module contents
• dmriprep.utils package
  • Submodules
  • dmriprep.utils.bids module
    • Utilities to handle BIDS inputs
  • dmriprep.utils.hemisphere module
  • Module contents
• dmriprep.viz package
  • Submodules
  • dmriprep.viz.utils module
  • Module contents
• dmriprep.workflows package
  • Subpackages
    • dmriprep.workflows.dwi package
      • Submodules
      • dmriprep.workflows.dwi.artifacts module
        • Artefact removal and resizing
      • dmriprep.workflows.dwi.base module
        • Orchestrating the dwi preprocessing workflows
      • dmriprep.workflows.dwi.eddy module
        • Head motion, eddy current distortion and EPI distortion correction
      • dmriprep.workflows.dwi.outputs module
        • Output dwi
      • dmriprep.workflows.dwi.qc module
      • dmriprep.workflows.dwi.tensor module
        • Tensor fitting
      • dmriprep.workflows.dwi.util module
        • Utility workflows
      • Module contents
        • Pre-processing dMRI workflows
          • Orchestrating the dwi preprocessing workflows
          • Utility workflows
          • Artefact removal and resizing
          • Head motion, eddy current distortion and EPI distortion correction
          • Tensor fitting
          • Output dwi
    • dmriprep.workflows.fieldmap package
      • Submodules
      • dmriprep.workflows.fieldmap.base module
      • dmriprep.workflows.fieldmap.brainsuite module
        • SDC using BrainSuite
      • dmriprep.workflows.fieldmap.fmap module
      • dmriprep.workflows.fieldmap.pepolar module
      • dmriprep.workflows.fieldmap.phasediff module
      • dmriprep.workflows.fieldmap.synb0 module
      • Module contents
  • Submodules
  • dmriprep.workflows.anatomical module
    • Orchestrating the T1w preprocessing workflows
  • dmriprep.workflows.base module
    • dMRIprep base processing workflows
  • Module contents

Submodules

dmriprep.cli module

Console script for dmriprep.

dmriprep.due module

Stub file for a guaranteed safe import of duecredit constructs: if duecredit is not available.

To use it, place it into your project codebase to be imported, e.g. copy as

cp stub.py /path/tomodule/module/due.py

Note that it might be better to avoid naming it duecredit.py to avoid shadowing installed duecredit.

Then use in your code as

from .due import due, Doi, BibTeX, Text

See https://github.com/duecredit/duecredit/blob/master/README.md for examples.

Origin: Originally a part of the duecredit Copyright: 2015-2019 DueCredit developers License: BSD-2

dmriprep.due.BibTeX(*args, **kwargs)

Perform no good and no bad

dmriprep.due.Doi(*args, **kwargs)

Perform no good and no bad

class dmriprep.due.InactiveDueCreditCollector

Bases: object

Just a stub at the Collector which would not do anything

activate(*args, **kwargs)

Perform no good and no bad

active = False

add(*args, **kwargs)

Perform no good and no bad

cite(*args, **kwargs)

Perform no good and no bad

dcite(*args, **kwargs)

If I could cite I would

dump(*args, **kwargs)

Perform no good and no bad

load(*args, **kwargs)

Perform no good and no bad

dmriprep.due.Text(*args, **kwargs)

Perform no good and no bad

dmriprep.due.Url(*args, **kwargs)

Perform no good and no bad

dmriprep.qc module

dmriprep.qc.createB0_ColorFA_Mask_Sprites(b0_file, colorFA_file, mask_file)

dmriprep.qc.createSprite4D(dwi_file)

dmriprep.qc.create_report_json(dwi_corrected_file, eddy_rms, eddy_report, color_fa_file, anat_mask_file, outlier_indices, eddy_qc_file, outpath='/home/docs/checkouts/readthedocs.org/user_builds/dmriprep-personal/checkouts/refactor/docs/report.json')

dmriprep.qc.create_sprite_from_tiles(tile, out_file=None, as_bytes=False)

dmriprep.qc.get_middle_slices(data, slice_direction)

dmriprep.qc.load_and_reorient(filename)

dmriprep.qc.mplfig(data, outfile=None, as_bytes=False)

dmriprep.qc.mplfigcontour(data, outfile=None, as_bytes=False)

dmriprep.qc.nearest_square(limit)

dmriprep.qc.reorient_array(data, aff)

dmriprep.qc.reshape3D(data, n=256)

dmriprep.qc.reshape4D(data, n=256)

Module contents

Top-level package for dmriprep.