remove tbss and update docs

Author: josephmje

dmriprep/cli.py

@@ -34,9 +34,7 @@ def __init__(
         omp_nthreads,
         eddy_niter,
         synb0_dir,
-        acqp_file,
-        tbss,
-        diffusivity_meas,
+        acqp_file
     ):
 
         self.layout = layout
@@ -54,8 +52,6 @@ def __init__(
         self.eddy_niter = eddy_niter
         self.synb0_dir = synb0_dir
         self.acqp_file = acqp_file
-        self.tbss = (tbss,)
-        self.diffusivity_meas = diffusivity_meas
 
 
 @click.command()
@@ -155,14 +151,6 @@ def __init__(
     help="working directory",
     type=click.Path(exists=True, file_okay=False, writable=True),
 )
-@click.option("--tbss", help="Run TBSS", is_flag=True)
-@click.option(
-    "--diffusivity_meas",
-    help="Specify which measures to calculate.",
-    default=("FA",),
-    type=click.Choice(["FA", "MD", "AD", "RD"]),
-    multiple=True,
-)
 @click.option(
     "--synb0_dir",
     default=None,
@@ -184,9 +172,7 @@ def main(
     omp_nthreads,
     eddy_niter,
     synb0_dir,
-    acqp_file,
-    tbss,
-    diffusivity_meas,
+    acqp_file
 ):
     """
     BIDS_DIR: The directory with the input dataset formatted according to the
@@ -238,9 +224,7 @@ def main(
         omp_nthreads=omp_nthreads,
         eddy_niter=eddy_niter,
         synb0_dir=synb0_dir,
-        acqp_file=acqp_file,
-        tbss=tbss,
-        diffusivity_meas=list(diffusivity_meas),
+        acqp_file=acqp_file
     )
 
     wf = init_dmriprep_wf(parameters)

dmriprep/workflows/base.py

@@ -25,7 +25,7 @@ def init_dmriprep_wf(parameters):
         single_subject_wf = init_single_subject_wf(
             subject_id=subject_id,
             name="single_subject_" + subject_id + "_wf",
-            parameters=parameters,
+            parameters=parameters
         )
 
         single_subject_wf.config["execution"]["crashdump_dir"] = os.path.join(
@@ -47,7 +47,7 @@ def init_single_subject_wf(subject_id, name, parameters):
         datatype="dwi",
         suffix="dwi",
         extensions=[".nii", ".nii.gz"],
-        return_type="filename",
+        return_type="filename"
     )
 
     if not dwi_files:
@@ -69,12 +69,12 @@ def init_single_subject_wf(subject_id, name, parameters):
             subject_id=subject_id,
             dwi_file=dwi_file,
             metadata=metadata,
-            parameters=parameters,
+            parameters=parameters
         )
         datasink_wf = init_output_wf(
             subject_id=subject_id,
             session_id=session_id,
-            output_folder=parameters.output_dir,
+            output_folder=parameters.output_dir
         )
 
         dwi_preproc_wf.base_dir = os.path.join(
@@ -120,8 +120,8 @@ def init_single_subject_wf(subject_id, name, parameters):
                         ("outputnode.out_dtifit_FA", "inputnode.dtifit_FA"),
                         ("outputnode.out_dtifit_V1", "inputnode.dtifit_V1"),
                         ("outputnode.out_dtifit_sse", "inputnode.dtifit_sse"),
-                        ("outputnode.out_noise", "inputnode.noise"),
-                    ],
+                        ("outputnode.out_noise", "inputnode.noise")
+                    ]
                 )
             ]
         )

dmriprep/workflows/dwi/__init__.py

@@ -1,6 +1,25 @@
 #!/usr/bin/env python
 
+"""
+
+Pre-processing dMRI workflows
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: dmriprep.workflows.dwi.base
+.. automodule:: dmriprep.workflows.dwi.prep_dwi
+.. automodule:: dmriprep.workflows.dwi.tensor
+.. automodule:: dmriprep.workflows.dwi.outputs
+
+"""
+
 from .base import init_dwi_preproc_wf
 from .prep_dwi import init_prep_dwi_wf
 from .tensor import init_tensor_wf
 from .outputs import init_output_wf
+
+__all__ = [
+    "init_dwi_preproc_wf",
+    "init_prep_dwi_wf",
+    "init_tensor_wf",
+    "init_output_wf"
+]

dmriprep/workflows/dwi/base.py

@@ -4,6 +4,8 @@
 Orchestrating the dwi preprocessing workflows
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+.. autofunction:: init_dwi_preproc_wf
+
 """
 
 from bids import BIDSLayout
@@ -52,7 +54,16 @@ def init_dwi_preproc_wf(subject_id, dwi_file, metadata, parameters):
     #     synb0,
     # )
 
-    dwi_wf = pe.Workflow(name="dwi_preproc_wf")
+    multiple_runs = isinstance(dwi_file, list)
+
+    if multiple_runs:
+        ref_file = dwi_file[0]
+    else:
+        ref_file = dwi_file
+
+    wf_name = _get_wf_name(ref_file)
+
+    dwi_wf = pe.Workflow(name=wf_name)
 
     inputnode = pe.Node(
         niu.IdentityInterface(
@@ -419,3 +430,19 @@ def get_b0_mask_fn(b0_file):
     )
 
     return dwi_wf
+
+
+def _get_wf_name(dwi_fname):
+    """
+    Derives the workflow name from the supplied dwi file.
+    """
+
+    from nipype.utils.filemanip import split_filename
+
+    fname = split_filename(dwi_fname)[1]
+    fname_nosub = "_".join(fname.split("_")[1:])
+    name = "func_preproc_" + fname_nosub.replace(".", "_").replace(" ", "").replace(
+        "-", "_"
+    ).replace("_dwi", "_wf")
+
+    return name

long_description.rst

@@ -28,4 +28,4 @@ segmentation, skullstripping etc.) providing outputs that can be
 easily submitted to a variety of tractography algorithms.
 
 [Documentation `dmriprep.org <https://dmriprep.readthedocs.io>`_]
-[Support `neurostars.org <https://neurostars.org/tags/fmriprep>`_]
+[Support `neurostars.org <https://neurostars.org/tags/dmriprep>`_]