Merge pull request #131 from oesteban/enh/remove-fmriprep-dep

ENH: Use ``bbregister`` upstreamed to NiWorkflows, with sloppy mode

Author: oesteban

dmriprep/workflows/base.py

@@ -8,11 +8,11 @@
 from nipype.interfaces import utility as niu
 
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
+from niworkflows.anat.coregistration import init_bbreg_wf
 from niworkflows.interfaces.bids import BIDSInfo, BIDSFreeSurferDir
 from niworkflows.utils.misc import fix_multi_T1w_source_name
 from niworkflows.utils.spaces import Reference
 from smriprep.workflows.anatomical import init_anat_preproc_wf
-from fmriprep.workflows.bold.registration import init_bbreg_wf
 
 from ..interfaces import DerivativesDataSink, BIDSDataGrabber
 from ..interfaces.reports import SubjectSummary, AboutSummary
@@ -362,10 +362,9 @@ def init_single_subject_wf(subject_id):
         t1w_brain = pe.Node(ApplyMask(), name="t1w_brain")
 
         bbr_wf = init_bbreg_wf(
-            bold2t1w_dof=6,
-            bold2t1w_init=config.workflow.dwi2t1w_init,
+            debug=config.execution.debug,
+            epi2t1w_init=config.workflow.dwi2t1w_init,
             omp_nthreads=config.nipype.omp_nthreads,
-            use_bbr=True,
         )
 
         ds_report_reg = pe.Node(
@@ -388,8 +387,6 @@ def _bold_reg_suffix(fallback):
             (early_b0ref_wf, bbr_wf, [
                 ("outputnode.dwi_reference", "inputnode.in_file")
             ]),
-            (t1w_brain, bbr_wf, [("out_file", "inputnode.t1w_brain")]),
-            (anat_preproc_wf, bbr_wf, [("outputnode.t1w_dseg", "inputnode.t1w_dseg")]),
             (fsinputnode, bbr_wf, [("subjects_dir", "inputnode.subjects_dir")]),
             (bids_info, bbr_wf, [(("subject", _prefix), "inputnode.subject_id")]),
             (anat_preproc_wf, bbr_wf, [

docs/requirements.txt

@@ -1,9 +1,8 @@
 git+https://github.com/AleksandarPetrov/napoleon.git@0dc3f28a309ad602be5f44a9049785a1026451b3#egg=sphinxcontrib-napoleon
 git+https://github.com/rwblair/sphinxcontrib-versioning.git@39b40b0b84bf872fc398feff05344051bbce0f63#egg=sphinxcontrib-versioning
-fmriprep
 nbsphinx
-nipype ~= 1.4
-git+https://github.com/nipreps/niworkflows.git@master#egg=niworkflows
+nipype ~= 1.5.1
+git+https://github.com/oesteban/niworkflows.git@cc328fee37266985ed3f9f7ca42f3e3f1ac26487#egg=niworkflows
 packaging
 pydot>=1.2.3
 pydotplus

setup.cfg

@@ -25,15 +25,14 @@ install_requires =
     indexed_gzip >=0.8.8
     nibabel ~= 3.0
     nipype ~= 1.5.1
-    niworkflows ~= 1.3.2
+    niworkflows @ git+https://github.com/oesteban/niworkflows.git@cc328fee37266985ed3f9f7ca42f3e3f1ac26487
     numpy
     pybids >= 0.11.1
     pyyaml
     sdcflows ~= 1.3.3
     smriprep ~= 0.7.0 
     templateflow ~= 0.6
     toml
-    fmriprep ~= 20.2
 setup_requires =
     setuptools >= 40.8.0
 test_requires =