update docs and doctests

Author: josephmje

dmriprep/data/tests/dwi_mask.nii.gz

@@ -20,17 +20,16 @@ class ExtractB0OutputSpec(TraitedSpec):
 
 class ExtractB0(SimpleInterface):
     """
+    Extract all b=0 volumes from a dwi series.
 
     Example
     -------
 
     >>> os.chdir(tmpdir)
     >>> extract_b0 = ExtractB0()
     >>> extract_b0.inputs.in_file = str(data_dir / 'dwi.nii.gz')
-    >>> extract_b0.inputs.b0_ixs = [0, 9, 18, 27, 36, 45, 54, 63, 72, 81, 90, 100]
-    >>> res = extract_b0.run()
-    >>> import nibabel as nb
-    >>> nb.load(res.outputs.out_file).shape
+    >>> extract_b0.inputs.b0_ixs = [0, 1, 2]
+    >>> res = extract_b0.run()  # doctest: +SKIP
 
     """
     input_spec = ExtractB0InputSpec
@@ -76,6 +75,20 @@ class RescaleB0OutputSpec(TraitedSpec):
 
 
 class RescaleB0(SimpleInterface):
+    """
+    Rescale the b0 volumes to deal with average signal decay over time
+    and output the median image.
+
+    Example
+    -------
+
+    >>> os.chdir(tmpdir)
+    >>> rescale_b0 = RescaleB0()
+    >>> rescale_b0.inputs.in_file = str(data_dir / 'dwi.nii.gz')
+    >>> rescale_b0.inputs.mask_file = str(data_dir / 'dwi_mask.nii.gz')
+    >>> res = rescale_b0.run()  # doctest: +SKIP
+
+    """
 
     input_spec = RescaleB0InputSpec
     output_spec = RescaleB0OutputSpec
@@ -90,10 +103,7 @@ def _run_interface(self, runtime):
 
 def rescale_b0(in_file, mask_file, newpath=None):
     """
-    Rescale the b0 volumes to deal with average signal decay over time
-    and calculate the median.
-    """
-    from dipy.segment.mask import applymask
+    Rescale the *b0* volumes from a DWI dataset."""
     import numpy as np
     import nibabel as nib
     from nipype.utils.filemanip import fname_presuffix

dmriprep/interfaces/images.py

@@ -26,6 +26,13 @@ def init_dwi_reference_wf(omp_nthreads, dwi_file=None,
     """
     Build a workflow that generates a reference b0 image from a dwi series.
 
+    To generate the reference b0, this workflow takes in a dwi series,
+    extracts the b0s, registers them to eachother, rescales the signal
+    intensity values, and calculates a median image.
+
+    Then, the reference b0 and its skull-stripped version are generated using
+    a custom methodology taken from *niworkflows*.
+
     .. workflow::
         :graph2use: orig
         :simple_form: yes
@@ -73,10 +80,7 @@ def init_dwi_reference_wf(omp_nthreads, dwi_file=None,
 
     """
     workflow = Workflow(name=name)
-    workflow.__desc__ = """\
-First, a reference volume and its skull-stripped version were generated
-using a custom methodology taken from *fMRIPrep*.
-"""
+
     inputnode = pe.Node(niu.IdentityInterface(fields=['dwi_file', 'b0_ixs']),
                         name='inputnode')
     outputnode = pe.Node(
@@ -133,16 +137,6 @@ def init_dwi_reference_wf(omp_nthreads, dwi_file=None,
     return workflow
 
 
-def init_b0_template_wf(
-    name='b0_template_wf'
-):
-   """[summary]
-
-   Keyword Arguments:
-       name {str} -- [description] (default: {'b0_template_wf'})
-   """
-
-
 def init_enhance_and_skullstrip_dwi_wf(
         name='enhance_and_skullstrip_dwi_wf',
         omp_nthreads=1):