fix: Pass the un-saved fmap_mask, remove from inputs

Author: effigies

fmriprep/workflows/base.py

@@ -732,6 +732,7 @@ def init_single_subject_wf(
             'fmap': 'fmap_derivatives_wf.ds_fieldmap.out_file',
             'fmap_ref': 'fmap_derivatives_wf.ds_reference.out_file',
             'fmap_coeff': 'fmap_derivatives_wf.ds_coeff.out_file',
+            'fmap_mask': 'outputnode.fmap_mask',
         }
 
         workflow.connect([

fmriprep/workflows/bold/fit.py

@@ -511,7 +511,7 @@ def init_bold_fit_wf(
 
             itk_mat2txt = pe.Node(ConcatenateXFMs(out_fmt='itk'), name='itk_mat2txt')
             fmapreg_source_files = pe.Node(
-                niu.Merge(3), name='fmapreg_source_files', run_without_submitting=True
+                niu.Merge(2), name='fmapreg_source_files', run_without_submitting=True
             )
 
             ds_fmapreg_wf = init_ds_registration_wf(
@@ -532,7 +532,6 @@ def init_bold_fit_wf(
                 (fmapref_buffer, fmapreg_source_files, [('out', 'in1')]),
                 (fmap_select, fmapreg_source_files, [
                     ('fmap_ref', 'in2'),
-                    ('fmap_mask', 'in3'),
                 ]),
                 (fmapreg_wf, itk_mat2txt, [('outputnode.target2fmap_xfm', 'in_xfms')]),
                 (itk_mat2txt, ds_fmapreg_wf, [('out_xfm', 'inputnode.xform')]),