wip

Author: josephmje

dmriprep/workflows/dwi/base.py

@@ -4,8 +4,6 @@
 Orchestrating the dwi preprocessing workflows
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. autofunction:: init_dwi_preproc_wf
-
 """
 
 from bids import BIDSLayout
@@ -93,6 +91,14 @@ def init_dwi_preproc_wf(subject_id, dwi_file, metadata, parameters):
         name="outputnode",
     )
 
+    denoise = pe.Node(mrtrix3.DWIDenoise(), name="denoise")
+
+    unring = pe.Node(mrtrix3.MRDeGibbs(), name="unring")
+
+    resample = pe.Node(
+        mrtrix3.MRResize(voxel_size=parameters.output_resolution), name="resample"
+    )
+
     def gen_index(in_file):
         import os
         import numpy as np
@@ -101,10 +107,7 @@ def gen_index(in_file):
         from nipype.utils.filemanip import fname_presuffix
 
         out_file = fname_presuffix(
-            in_file,
-            suffix="_index.txt",
-            newpath=os.path.abspath("."),
-            use_ext=False,
+            in_file, suffix="_index.txt", newpath=os.path.abspath("."), use_ext=False
         )
         vols = nib.load(in_file, mmap=NUMPY_MMAP).get_data().shape[-1]
         index_lines = np.ones((vols,))
@@ -114,9 +117,7 @@ def gen_index(in_file):
 
     gen_idx = pe.Node(
         niu.Function(
-            input_names=["in_file"],
-            output_names=["out_file"],
-            function=gen_index,
+            input_names=["in_file"], output_names=["out_file"], function=gen_index
         ),
         name="gen_index",
     )
@@ -162,11 +163,7 @@ def gen_acqparams(in_file, metadata):
     dwi_wf.connect(
         [
             (inputnode, gen_idx, [("dwi_file", "in_file")]),
-            (
-                inputnode,
-                acqp,
-                [("dwi_file", "in_file"), ("dwi_meta", "metadata")],
-            ),
+            (inputnode, acqp, [("dwi_file", "in_file"), ("dwi_meta", "metadata")]),
         ]
     )
 
@@ -215,13 +212,10 @@ def b0_average(in_dwi, in_bval, b0_thresh, out_file=None):
     avg_b0_0.inputs.b0_thresh = parameters.b0_thresh
 
     bet_dwi0 = pe.Node(
-        fsl.BET(frac=parameters.bet_dwi, mask=True, robust=True),
-        name="bet_dwi_pre",
+        fsl.BET(frac=parameters.bet_dwi, mask=True, robust=True), name="bet_dwi_pre"
     )
 
-    ecc = pe.Node(
-        fsl.Eddy(repol=True, cnr_maps=True, residuals=True), name="fsl_eddy"
-    )
+    ecc = pe.Node(fsl.Eddy(repol=True, cnr_maps=True, residuals=True), name="fsl_eddy")
 
     if parameters.omp_nthreads:
         ecc.inputs.num_threads = parameters.omp_nthreads
@@ -290,9 +284,7 @@ def b0_average(in_dwi, in_bval, b0_thresh, out_file=None):
     fslroi = pe.Node(fsl.ExtractROI(t_min=0, t_size=1), name="fslroi")
 
     bias_correct = pe.Node(
-        ants.N4BiasFieldCorrection(
-            save_bias=True, copy_header=True, dimension=3
-        ),
+        ants.N4BiasFieldCorrection(save_bias=True, copy_header=True, dimension=3),
         name="bias_correct",
     )
 
@@ -313,9 +305,7 @@ def get_b0_mask_fn(b0_file):
 
     b0mask_node = pe.Node(
         niu.Function(
-            input_names=["b0_file"],
-            output_names=["mask_file"],
-            function=get_b0_mask_fn,
+            input_names=["b0_file"], output_names=["mask_file"], function=get_b0_mask_fn
         ),
         name="getB0Mask",
     )
@@ -324,11 +314,7 @@ def get_b0_mask_fn(b0_file):
         [
             (inputnode, avg_b0_0, [("bval_file", "in_bval")]),
             (avg_b0_0, bet_dwi0, [("out_file", "in_file")]),
-            (
-                inputnode,
-                ecc,
-                [("bval_file", "in_bval"), ("bvec_file", "in_bvec")],
-            ),
+            (inputnode, ecc, [("bval_file", "in_bval"), ("bvec_file", "in_bvec")]),
             (bet_dwi0, ecc, [("mask_file", "in_mask")]),
             (gen_idx, ecc, [("out_file", "in_index")]),
             (acqp, ecc, [("out_file", "in_acqp")]),
@@ -440,10 +426,7 @@ def get_b0_mask_fn(b0_file):
             (
                 eddy_quad,
                 outputnode,
-                [
-                    ("qc_json", "out_eddy_quad_json"),
-                    ("qc_pdf", "out_eddy_quad_pdf"),
-                ],
+                [("qc_json", "out_eddy_quad_json"), ("qc_pdf", "out_eddy_quad_pdf")],
             ),
             (
                 tensor_wf,

dmriprep/workflows/dwi/denoise.py

@@ -8,13 +8,9 @@ def init_denoise_wf():
 
     wf = pe.Workflow(name="denoise_wf")
 
-    inputnode = pe.Node(
-        niu.IdentityInterface(fields=["dwi_file"]), name="inputnode"
-    )
+    inputnode = pe.Node(niu.IdentityInterface(fields=["dwi_file"]), name="inputnode")
 
-    outputnode = pe.Node(
-        niu.IdentityInterface(fields=["out_file"]), name="outputnode"
-    )
+    outputnode = pe.Node(niu.IdentityInterface(fields=["out_file"]), name="outputnode")
 
     denoise = pe.Node(mrtrix3.DWIDenoise(), name="denoise")