enh: final integration stretch - pin deps, cleanup

nipreps · Mar 9, 2021 · c50afb9 · c50afb9
1 parent 6832fdf
commit c50afb9
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Showing 5 changed files with 26 additions and 23 deletions.
diff --git a/dmriprep/cli/workflow.py b/dmriprep/cli/workflow.py
@@ -139,8 +139,7 @@ def build_boilerplate(config_file, workflow):
             "-s",
             "--bibliography",
             pkgrf("dmriprep", "data/boilerplate.bib"),
-            "--filter",
-            "pandoc-citeproc",
+            "--citeproc",
             "--metadata",
             'pagetitle="dMRIPrep citation boilerplate"',
             str(citation_files["md"]),

diff --git a/dmriprep/config/reports-spec.yml b/dmriprep/config/reports-spec.yml
@@ -26,7 +26,7 @@ sections:
     caption: Surfaces (white and pial) reconstructed with FreeSurfer (<code>recon-all</code>)
       overlaid on the participant's T1w template.
     subtitle: Surface reconstruction
-- name: Fieldmaps
+- name: <em>B<sub>0</sub></em> field mapping
   ordering: session,run,fmapid
   reportlets:
   - bids: {datatype: figures, desc: mapped, suffix: fieldmap}
@@ -38,7 +38,7 @@ sections:
     description: Hover over the panels with the mouse pointer to also visualize the intensity of the
       field inhomogeneity in Hertz.
     static: false
-    subtitle: "Susceptibility-derived Distortion Correction (SDC): field inhomogeneity estimation"
+    subtitle: "Preprocessed <em>B<sub>0</sub></em> mapping acquisition"
   - bids: {datatype: figures, desc: phasediff, suffix: fieldmap}
     caption: Inhomogeneities of the <em>B<sub>0</sub></em> field introduce (oftentimes severe) spatial distortions
       along the phase-encoding direction of the image. A Gradient-Recalled Echo (GRE) scheme for the 
@@ -48,7 +48,7 @@ sections:
     description: Hover over the panels with the mouse pointer to also visualize the intensity of the
       field inhomogeneity in Hertz.
     static: false
-    subtitle: "Susceptibility-derived Distortion Correction (SDC): field inhomogeneity estimation"
+    subtitle: "Preprocessed mapping of phase-difference acquisition"
   - bids: {datatype: figures, desc: pepolar, suffix: fieldmap}
     caption: Inhomogeneities of the <em>B<sub>0</sub></em> field introduce (oftentimes severe) spatial distortions
       along the phase-encoding direction of the image. Utilizing two or more images with different
@@ -58,7 +58,17 @@ sections:
     description: Hover on the panels with the mouse pointer to also visualize the intensity of the
       inhomogeneity of the field in Hertz.
     static: false
-    subtitle: "Susceptibility-derived Distortion Correction (SDC): field inhomogeneity estimation"
+    subtitle: "Preprocessed estimation with varying Phase-Endocing (PE) blips"
+  - bids: {datatype: figures, desc: anat, suffix: fieldmap}
+    caption: Inhomogeneities of the <em>B<sub>0</sub></em> field introduce (oftentimes severe) spatial distortions
+      along the phase-encoding direction of the image. Utilizing an <em>anatomically-correct</em> acquisition
+      (for instance, T1w or T2w), it is possible to estimate the inhomogeneity of the field by means of nonlinear
+      registration. The plot below shows a reference EPI (echo-planar imaging) volume generated
+      using two or more EPI images with the same PE encoding, after alignment to the anatomical scan.
+    description: Hover on the panels with the mouse pointer to also visualize the intensity of the
+      inhomogeneity of the field in Hertz.
+    static: false
+    subtitle: "Preprocessed estimation by nonlinear registration to an anatomical scan (&ldquo;<em>fieldmap-less</em>&rdquo;)"
 - name: Diffusion
   ordering: session,acquisition,run
   reportlets:

diff --git a/dmriprep/workflows/base.py b/dmriprep/workflows/base.py
@@ -368,7 +368,7 @@ def init_single_subject_wf(subject_id):
 
     # SDC Step 2: Manually add further estimators (e.g., fieldmap-less)
     fmap_wf = init_fmap_preproc_wf(
-        debug=config.execution.debug,
+        debug=config.execution.debug is True,
         estimators=fmap_estimators,
         omp_nthreads=config.nipype.omp_nthreads,
         output_dir=str(output_dir),
@@ -424,8 +424,6 @@ def init_single_subject_wf(subject_id):
             )
 
         if estimator.method == fm.EstimatorType.ANAT:
-            from niworkflows.utils.connections import pop_file as _pop
-            from sdcflows.interfaces.brainmask import BrainExtraction
             from sdcflows.workflows.fit.syn import init_syn_preprocessing_wf
             from ..interfaces.vectors import CheckGradientTable
 
@@ -436,6 +434,7 @@ def init_single_subject_wf(subject_id):
             layout = config.execution.layout
             syn_preprocessing_wf = init_syn_preprocessing_wf(
                 omp_nthreads=config.nipype.omp_nthreads,
+                debug=config.execution.debug is True,
                 auto_bold_nss=False,
                 t1w_inversion=True,
                 name=f"syn_preprocessing_{estimator.bids_id}",
@@ -450,26 +449,21 @@ def init_single_subject_wf(subject_id):
             b0_masks.inputs.in_bvec = [str(layout.get_bvec(s)) for s in sources]
             b0_masks.inputs.in_bval = [str(layout.get_bval(s)) for s in sources]
 
-            epi_brain = pe.Node(BrainExtraction(), name=f"epi_brain_{estimator.bids_id}")
-
             # fmt:off
             workflow.connect([
                 (anat_preproc_wf, syn_preprocessing_wf, [
                     ("outputnode.t1w_preproc", "inputnode.in_anat"),
                     ("outputnode.t1w_mask", "inputnode.mask_anat"),
+                    ("outputnode.std2anat_xfm", f"inputnode.std2anat_xfm"),
                 ]),
                 (b0_masks, syn_preprocessing_wf, [("b0_mask", "inputnode.t_masks")]),
                 (syn_preprocessing_wf, fmap_wf, [
                     ("outputnode.epi_ref", f"in_{estimator.bids_id}.epi_ref"),
+                    ("outputnode.epi_mask", f"in_{estimator.bids_id}.epi_mask"),
                     ("outputnode.anat_ref", f"in_{estimator.bids_id}.anat_ref"),
-                    ("outputnode.anat2epi_xfm", f"in_{estimator.bids_id}.anat2epi_xfm"),
-                ]),
-                (syn_preprocessing_wf, epi_brain, [
-                    (("outputnode.epi_ref", _pop), "in_file")]),
-                (anat_preproc_wf, fmap_wf, [
-                    ("outputnode.std2anat_xfm", f"in_{estimator.bids_id}.std2anat_xfm"),
+                    ("outputnode.anat_mask", f"in_{estimator.bids_id}.anat_mask"),
+                    ("outputnode.sd_prior", f"in_{estimator.bids_id}.sd_prior"),
                 ]),
-                (epi_brain, fmap_wf, [("out_mask", f"in_{estimator.bids_id}.epi_mask")]),
             ])
             # fmt:on
 

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -2,15 +2,15 @@ git+https://github.com/AleksandarPetrov/napoleon.git@0dc3f28a309ad602be5f44a9049
 git+https://github.com/rwblair/sphinxcontrib-versioning.git@39b40b0b84bf872fc398feff05344051bbce0f63#egg=sphinxcontrib-versioning
 nbsphinx
 nipype ~= 1.5.1
-niworkflows >=1.4.0rc0,<1.5
+niworkflows >=1.4.0rc5,<1.5
 packaging
 pydot>=1.2.3
 pydotplus
-sdcflows ~= 2.0.0
+sdcflows ~= 2.0
 smriprep >= 0.8.0rc0
 sphinx >=2.1.2,<3.0
 sphinx-argparse
 sphinx_rtd_theme
 sphinxcontrib-apidoc ~= 0.3.0
 templateflow
-toml
+toml
diff --git a/setup.cfg b/setup.cfg
@@ -25,11 +25,11 @@ install_requires =
     indexed_gzip >=0.8.8
     nibabel ~= 3.0
     nipype >= 1.5.1, < 2.0
-    niworkflows @ git+https://github.com/nipreps/niworkflows.git@master
+    niworkflows >=1.4.0rc5, <1.5 
     numpy
     pybids >= 0.11.1
     pyyaml
-    sdcflows @ git+https://github.com/nipreps/sdcflows.git@ca69ff15a5cf12522fa75a2a2ed4247af0713560
+    sdcflows ~= 2.0.1
     smriprep >= 0.8.0rc0
     svgutils != 0.3.2
     templateflow ~= 0.6