update docs

Author: josephmje

docs/dmriprep.workflows.fieldmap.rst

@@ -4,6 +4,14 @@ dmriprep.workflows.fieldmap package
 Submodules
 ----------
 
+dmriprep.workflows.fieldmap.ants module
+---------------------------------------
+
+.. automodule:: dmriprep.workflows.fieldmap.ants
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 dmriprep.workflows.fieldmap.base module
 ---------------------------------------
 
@@ -12,6 +20,14 @@ dmriprep.workflows.fieldmap.base module
    :undoc-members:
    :show-inheritance:
 
+dmriprep.workflows.fieldmap.brainsuite module
+---------------------------------------------
+
+.. automodule:: dmriprep.workflows.fieldmap.brainsuite
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 dmriprep.workflows.fieldmap.fmap module
 ---------------------------------------
 
@@ -36,6 +52,14 @@ dmriprep.workflows.fieldmap.phasediff module
    :undoc-members:
    :show-inheritance:
 
+dmriprep.workflows.fieldmap.synb0 module
+----------------------------------------
+
+.. automodule:: dmriprep.workflows.fieldmap.synb0
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 
 Module contents
 ---------------

docs/index.rst

@@ -13,9 +13,3 @@
    sdc
    outputs
    contributing
-
-Indices and tables
-==================
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

docs/workflows.rst

@@ -1,2 +1,69 @@
 Processing pipeline details
 ===========================
+
+dMRIprep adapts its pipeline depending on what data and metadata are available and are used as the input.
+
+A (very) high-level view of the simplest pipeline is presented below.
+
+.. workflow::
+    :graph2use: orig
+    :simple_form: yes
+
+    from collections import namedtuple, OrderedDict
+    from dmriprep.workflows.base import init_single_subject_wf
+    BIDSLayout = namedtuple('BIDSLayout', ['root'])
+    wf = init_single_subject_wf(
+        subject_id='test',
+        session_list=[],
+        name='single_subject_wf',
+        layout=BIDSLayout,
+        output_dir='.',
+        work_dir='.',
+        ignore=[],
+        b0_thresh=5,
+        output_resolution=(1, 1, 1),
+        bet_dwi=0.3,
+        bet_mag=0.3,
+        omp_nthreads=1,
+        synb0_dir=''
+    )
+
+T1w preprocessing
+-----------------
+:mod:`dmriprep.workflows.anatomical.init_anat_preproc_wf`
+
+.. workflow::
+    :graph2use: orig
+    :simple_form: yes
+
+    from collections import OrderedDict
+    from dmriprep.workflows.anatomical import init_anat_preproc_wf
+    wf = init_anat_preproc_wf()
+
+DWI preprocessing
+-----------------
+:mod:`dmriprep.workflows.dwi.base.init_dwi_preproc_wf`
+
+.. workflow::
+    :graph2use: orig
+    :simple_form: yes
+
+    from collections import namedtuple
+    from dmriprep.workflows.dwi import init_dwi_preproc_wf
+    BIDSLayout = namedtuple('BIDSLayout', ['root'])
+    wf = init_dwi_preproc_wf(
+        subjectid='dmripreptest',
+        dwi_file='/madeup/path/sub-01_dwi.nii.gz',
+        metadata={},
+        layout=BIDSLayout('.'),
+        ignore=[],
+        b0_thresh=5,
+        output_resolution=(1, 1, 1),
+        bet_dwi=0.3,
+        bet_mag=0.3,
+        nthreads=4,
+        omp_nthreads=1,
+        synb0_dir='.'
+    )
+
+Preprocessing of DWI files is split into multiple sub-workflows described below.

setup.cfg

@@ -1,9 +1,9 @@
 [metadata]
-url = https://github.com/nipreps/dmriprep
+url = https://github.com/josephmje/dmriprep
 author = The Nipy developers
-author_email = [email protected]
-maintainer = Oscar Esteban
-maintainer_email = [email protected]
+author_email = [email protected]
+maintainer = Michael Joseph
+maintainer_email = [email protected]
 description = dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data.
 long_description = file:long_description.rst
 long_description_content_type = text/x-rst; charset=UTF-8
@@ -22,26 +22,26 @@ python_requires = >=3.5
 install_requires =
     Click >= 7.0
     dipy ~= 1.0.0
-    nipype >=1.2.1
-    niworkflows ~= 0.10.1
-    smriprep @ git+https://github.com/poldracklab/smriprep.git@9f58665830570835545ff83fea1dc91e89706591
-    templateflow ~= 0.4.1
-    nibabel >=2.2.1
     indexed_gzip >=0.8.8
+    matplotlib
+    nibabel >=2.2.1
     nilearn !=0.5.0, !=0.5.1
-    psutil >=5.4
-    pybids ~= 0.9.2
+    nipype >=1.2.1
     nitime
+    niworkflows ~= 0.10.1
+    numba ~= 0.44.1
     numpy
     pandas
-    matplotlib
-    numba ~= 0.44.1
+    psutil >=5.4
+    pybids ~= 0.9.3
     pyyaml
     scikit-image
+    smriprep @ git+https://github.com/poldracklab/smriprep.git@9f58665830570835545ff83fea1dc91e89706591
     statsmodels
+    templateflow ~= 0.4.1
 test_requires =
-    coverage
     codecov
+    coverage
     pytest
 packages = find:
 include_package_data = True
@@ -64,8 +64,8 @@ docs =
 duecredit = duecredit
 resmon =
 tests =
-    coverage
     codecov
+    coverage
     pytest
 all =
     %(datalad)s
@@ -79,8 +79,6 @@ dmriprep =
     data/*.nii.gz
     data/*.mat
     data/boilerplate.bib
-    data/itkIdentityTransform.txt
-    data/flirtsch/bbr.sch
     VERSION
 
 [options.entry_points]