Merge pull request #1581 from oesteban/fix/issue-1579

FIX: Support 4D SBRefs when generating the bold reference

Author: oesteban

fmriprep/__about__.py

@@ -89,7 +89,7 @@
     'nilearn',
     'nipype>=1.1.6',
     'nitime',
-    'niworkflows<0.9.0a0,>=0.8.1',
+    'niworkflows',
     'numpy',
     'pandas',
     'psutil>=5.4',
@@ -104,6 +104,8 @@
 
 
 LINKS_REQUIRES = [
+    'git+https://github.com/poldracklab/niworkflows.git@'
+    'b7d111c8fd36a099c74be5e7671677eedb175533#egg=niworkflows',
     'git+https://github.com/poldracklab/smriprep.git@'
     '423bcc43ab7300177eb3b98da62817b2cad8eb87#egg=smriprep-0.1.0',
 ]

fmriprep/workflows/bold/base.py

@@ -338,15 +338,16 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
 """
 
     inputnode = pe.Node(niu.IdentityInterface(
-        fields=['bold_file', 'sbref_file', 'subjects_dir', 'subject_id',
+        fields=['bold_file', 'subjects_dir', 'subject_id',
                 't1_preproc', 't1_brain', 't1_mask', 't1_seg', 't1_tpms',
                 't1_aseg', 't1_aparc',
                 't1_2_mni_forward_transform', 't1_2_mni_reverse_transform',
                 't1_2_fsnative_forward_transform', 't1_2_fsnative_reverse_transform']),
         name='inputnode')
     inputnode.inputs.bold_file = bold_file
     if sbref_file is not None:
-        inputnode.inputs.sbref_file = sbref_file
+        from niworkflows.interfaces.images import ValidateImage
+        val_sbref = pe.Node(ValidateImage(in_file=sbref_file), name='val_sbref')
 
     outputnode = pe.Node(niu.IdentityInterface(
         fields=['bold_t1', 'bold_t1_ref', 'bold_mask_t1', 'bold_aseg_t1', 'bold_aparc_t1',
@@ -415,6 +416,10 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
 
     # Generate a tentative boldref
     bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads)
+    if sbref_file is not None:
+        workflow.connect([
+            (val_sbref, bold_reference_wf, [('out_file', 'inputnode.sbref_file')]),
+        ])
 
     # Top-level BOLD splitter
     bold_split = pe.Node(FSLSplit(dimension='t'), name='bold_split',
@@ -533,8 +538,7 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
     # MAIN WORKFLOW STRUCTURE #######################################################
     workflow.connect([
         # Generate early reference
-        (inputnode, bold_reference_wf, [('bold_file', 'inputnode.bold_file'),
-                                        ('sbref_file', 'inputnode.sbref_file')]),
+        (inputnode, bold_reference_wf, [('bold_file', 'inputnode.bold_file')]),
         # BOLD buffer has slice-time corrected if it was run, original otherwise
         (boldbuffer, bold_split, [('bold_file', 'in_file')]),
         # HMC

fmriprep/workflows/bold/util.py

@@ -115,8 +115,6 @@ def init_bold_reference_wf(omp_nthreads, bold_file=None, pre_mask=False,
 
     gen_ref = pe.Node(EstimateReferenceImage(), name="gen_ref",
                       mem_gb=1)  # OE: 128x128x128x50 * 64 / 8 ~ 900MB.
-    # Re-run validation; no effect if no sbref; otherwise apply same validation to sbref as bold
-    validate_ref = pe.Node(ValidateImage(), name='validate_ref', mem_gb=DEFAULT_MEMORY_MIN_GB)
     enhance_and_skullstrip_bold_wf = init_enhance_and_skullstrip_bold_wf(
         omp_nthreads=omp_nthreads, pre_mask=pre_mask)
 
@@ -125,12 +123,11 @@ def init_bold_reference_wf(omp_nthreads, bold_file=None, pre_mask=False,
         (inputnode, validate, [('bold_file', 'in_file')]),
         (inputnode, gen_ref, [('sbref_file', 'sbref_file')]),
         (validate, gen_ref, [('out_file', 'in_file')]),
-        (gen_ref, validate_ref, [('ref_image', 'in_file')]),
-        (validate_ref, enhance_and_skullstrip_bold_wf, [('out_file', 'inputnode.in_file')]),
+        (gen_ref,  enhance_and_skullstrip_bold_wf, [('ref_image', 'inputnode.in_file')]),
         (validate, outputnode, [('out_file', 'bold_file'),
                                 ('out_report', 'validation_report')]),
         (gen_ref, outputnode, [('n_volumes_to_discard', 'skip_vols')]),
-        (validate_ref, outputnode, [('out_file', 'raw_ref_image')]),
+        (gen_ref, outputnode, [('ref_image', 'raw_ref_image')]),
         (enhance_and_skullstrip_bold_wf, outputnode, [
             ('outputnode.bias_corrected_file', 'ref_image'),
             ('outputnode.mask_file', 'bold_mask'),

requirements.txt

@@ -1,3 +1,3 @@
-niworkflows<0.9.0a0,>=0.8.1
+git+https://github.com/poldracklab/niworkflows.git@b7d111c8fd36a099c74be5e7671677eedb175533#egg=niworkflows
 git+https://github.com/poldracklab/smriprep.git@423bcc43ab7300177eb3b98da62817b2cad8eb87#egg=smriprep-0.1.0
 templateflow<0.2.0a0,>=0.1.3