actually generate references

Author: oesteban

fmriprep/workflows/bold/base.py

@@ -347,10 +347,10 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
         inputnode.inputs.sbref_file = sbref_file
 
     outputnode = pe.Node(niu.IdentityInterface(
-        fields=['bold_t1', 'bold_mask_t1', 'bold_aseg_t1', 'bold_aparc_t1', 'cifti_variant',
-                'bold_mni', 'bold_mask_mni', 'bold_cifti', 'confounds', 'surfaces',
-                't2s_map', 'aroma_noise_ics', 'melodic_mix', 'nonaggr_denoised_file',
-                'cifti_variant_key']),
+        fields=['bold_t1', 'bold_t1_ref', 'bold_mask_t1', 'bold_aseg_t1', 'bold_aparc_t1',
+                'bold_mni', 'bold_mni_ref' 'bold_mask_mni', 'bold_cifti',
+                'cifti_variant', 'cifti_variant_key', 'confounds', 'surfaces',
+                't2s_map', 'aroma_noise_ics', 'melodic_mix', 'nonaggr_denoised_file']),
         name='outputnode')
 
     # BOLD buffer: an identity used as a pointer to either the original BOLD
@@ -376,10 +376,12 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
         (inputnode, func_derivatives_wf, [('bold_file', 'inputnode.source_file')]),
         (outputnode, func_derivatives_wf, [
             ('bold_t1', 'inputnode.bold_t1'),
+            ('bold_t1_ref', 'inputnode.bold_t1_ref'),
             ('bold_aseg_t1', 'inputnode.bold_aseg_t1'),
             ('bold_aparc_t1', 'inputnode.bold_aparc_t1'),
             ('bold_mask_t1', 'inputnode.bold_mask_t1'),
             ('bold_mni', 'inputnode.bold_mni'),
+            ('bold_mni_ref', 'inputnode.bold_mni_ref'),
             ('bold_mask_mni', 'inputnode.bold_mask_mni'),
             ('confounds', 'inputnode.confounds'),
             ('surfaces', 'inputnode.surfaces'),
@@ -501,6 +503,7 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
         (bold_reg_wf, bold_t1_trans_wf, [
             ('outputnode.itk_bold_to_t1', 'inputnode.itk_bold_to_t1')]),
         (bold_t1_trans_wf, outputnode, [('outputnode.bold_t1', 'bold_t1'),
+                                        ('outputnode.bold_t1_ref', 'bold_t1_ref'),
                                         ('outputnode.bold_aseg_t1', 'bold_aseg_t1'),
                                         ('outputnode.bold_aparc_t1', 'bold_aparc_t1')]),
         (bold_reg_wf, summary, [('outputnode.fallback', 'fallback')]),
@@ -676,6 +679,7 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
             (bold_sdc_wf, bold_mni_trans_wf, [
                 ('outputnode.out_warp', 'inputnode.fieldwarp')]),
             (bold_mni_trans_wf, outputnode, [('outputnode.bold_mni', 'bold_mni'),
+                                             ('outputnode.bold_mni_ref', 'bold_mni_ref'),
                                              ('outputnode.bold_mask_mni', 'bold_mask_mni')]),
             (bold_bold_trans_wf, carpetplot_wf, [
                 ('outputnode.bold', 'inputnode.bold'),
@@ -811,7 +815,9 @@ def init_func_derivatives_wf(output_dir, output_spaces, template, freesurfer,
 
     inputnode = pe.Node(
         niu.IdentityInterface(
-            fields=['source_file', 'bold_t1', 'bold_mask_t1', 'bold_mni', 'bold_mask_mni',
+            fields=['source_file',
+                    'bold_t1', 'bold_t1_ref', 'bold_mask_t1',
+                    'bold_mni', 'bold_mni_ref', 'bold_mask_mni',
                     'bold_aseg_t1', 'bold_aparc_t1', 'cifti_variant_key',
                     'confounds', 'surfaces', 'aroma_noise_ics', 'melodic_mix',
                     'nonaggr_denoised_file', 'bold_cifti', 'cifti_variant']),
@@ -847,6 +853,8 @@ def init_func_derivatives_wf(output_dir, output_spaces, template, freesurfer,
         workflow.connect([
             (inputnode, ds_bold_t1, [('source_file', 'source_file'),
                                      ('bold_t1', 'in_file')]),
+            (inputnode, ds_bold_t1_ref, [('source_file', 'source_file'),
+                                         ('bold_t1_ref', 'in_file')]),
             (inputnode, ds_bold_mask_t1, [('source_file', 'source_file'),
                                           ('bold_mask_t1', 'in_file')]),
         ])
@@ -869,6 +877,8 @@ def init_func_derivatives_wf(output_dir, output_spaces, template, freesurfer,
         workflow.connect([
             (inputnode, ds_bold_mni, [('source_file', 'source_file'),
                                       ('bold_mni', 'in_file')]),
+            (inputnode, ds_bold_mni_ref, [('source_file', 'source_file'),
+                                          ('bold_mni_ref', 'in_file')]),
             (inputnode, ds_bold_mask_mni, [('source_file', 'source_file'),
                                            ('bold_mask_mni', 'in_file')]),
         ])

fmriprep/workflows/bold/registration.py

@@ -112,8 +112,8 @@ def init_bold_reg_wf(freesurfer, use_bbr, bold2t1w_dof, mem_gb, omp_nthreads,
 
     **Subworkflows**
 
-        * :py:func:`~fmriprep.workflows.util.init_bbreg_wf`
-        * :py:func:`~fmriprep.workflows.util.init_fsl_bbr_wf`
+        * :py:func:`~fmriprep.workflows.bold.registration.init_bbreg_wf`
+        * :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`
 
     """
     workflow = Workflow(name=name)
@@ -232,6 +232,8 @@ def init_bold_t1_trans_wf(freesurfer, mem_gb, omp_nthreads, use_fieldwarp=False,
 
         bold_t1
             Motion-corrected BOLD series in T1 space
+        bold_t1_ref
+            Reference, contrast-enhanced summary of the motion-corrected BOLD series in T1w space
         bold_mask_t1
             BOLD mask in T1 space
         bold_aseg_t1
@@ -244,10 +246,11 @@ def init_bold_t1_trans_wf(freesurfer, mem_gb, omp_nthreads, use_fieldwarp=False,
 
     **Subworkflows**
 
-        * :py:func:`~fmriprep.workflows.util.init_bbreg_wf`
-        * :py:func:`~fmriprep.workflows.util.init_fsl_bbr_wf`
+        * :py:func:`~fmriprep.workflows.bold.registration.init_bbreg_wf`
+        * :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`
 
     """
+    from ..util import init_bold_reference_wf
     workflow = Workflow(name=name)
     inputnode = pe.Node(
         niu.IdentityInterface(
@@ -260,7 +263,7 @@ def init_bold_t1_trans_wf(freesurfer, mem_gb, omp_nthreads, use_fieldwarp=False,
 
     outputnode = pe.Node(
         niu.IdentityInterface(fields=[
-            'bold_t1', 'bold_mask_t1',
+            'bold_t1', 'bold_t1_ref', 'bold_mask_t1',
             'bold_aseg_t1', 'bold_aparc_t1']),
         name='outputnode'
     )
@@ -320,14 +323,19 @@ def init_bold_t1_trans_wf(freesurfer, mem_gb, omp_nthreads, use_fieldwarp=False,
 
     merge = pe.Node(Merge(compress=use_compression), name='merge', mem_gb=mem_gb)
 
+    # Generate a reference on the target T1w space
+    gen_final_ref = init_bold_reference_wf(omp_nthreads)
+
     workflow.connect([
         (inputnode, merge_xforms, [('itk_bold_to_t1', 'in1')]),
         (merge_xforms, bold_to_t1w_transform, [('out', 'transforms')]),
         (inputnode, merge, [('name_source', 'header_source')]),
         (inputnode, bold_to_t1w_transform, [('bold_split', 'input_image')]),
         (gen_ref, bold_to_t1w_transform, [('out_file', 'reference_image')]),
         (bold_to_t1w_transform, merge, [('out_files', 'in_files')]),
+        (merge, gen_final_ref, [('out_file', 'inputnode.bold_file')]),
         (merge, outputnode, [('out_file', 'bold_t1')]),
+        (gen_final_ref, outputnode, [('outputnode.ref_image', 'bold_t1_ref')]),
     ])
 
     return workflow
@@ -338,7 +346,7 @@ def init_bbreg_wf(use_bbr, bold2t1w_dof, omp_nthreads, name='bbreg_wf'):
     This workflow uses FreeSurfer's ``bbregister`` to register a BOLD image to
     a T1-weighted structural image.
 
-    It is a counterpart to :py:func:`~fmriprep.workflows.util.init_fsl_bbr_wf`,
+    It is a counterpart to :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`,
     which performs the same task using FSL's FLIRT with a BBR cost function.
 
     The ``use_bbr`` option permits a high degree of control over registration.
@@ -381,9 +389,9 @@ def init_bbreg_wf(use_bbr, bold2t1w_dof, omp_nthreads, name='bbreg_wf'):
         subject_id
             FreeSurfer subject ID (must have folder in SUBJECTS_DIR)
         t1_brain
-            Unused (see :py:func:`~fmriprep.workflows.util.init_fsl_bbr_wf`)
+            Unused (see :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`)
         t1_seg
-            Unused (see :py:func:`~fmriprep.workflows.util.init_fsl_bbr_wf`)
+            Unused (see :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`)
 
 
     Outputs
@@ -556,17 +564,17 @@ def init_fsl_bbr_wf(use_bbr, bold2t1w_dof, name='fsl_bbr_wf'):
         t1_seg
             FAST segmentation of ``t1_brain``
         t1_2_fsnative_reverse_transform
-            Unused (see :py:func:`~fmriprep.workflows.util.init_bbreg_wf`)
+            Unused (see :py:func:`~fmriprep.workflows.bold.registration.init_bbreg_wf`)
         subjects_dir
-            Unused (see :py:func:`~fmriprep.workflows.util.init_bbreg_wf`)
+            Unused (see :py:func:`~fmriprep.workflows.bold.registration.init_bbreg_wf`)
         subject_id
-            Unused (see :py:func:`~fmriprep.workflows.util.init_bbreg_wf`)
+            Unused (see :py:func:`~fmriprep.workflows.bold.registration.init_bbreg_wf`)
 
 
     Outputs
 
         itk_bold_to_t1
-            Affine transform from ``ref_bold_brain`` to T1 space (ITK format)
+            Affine transform from ``ref_bold_brain`` to T1w space (ITK format)
         itk_t1_to_bold
             Affine transform from T1 space to BOLD space (ITK format)
         out_report

fmriprep/workflows/bold/resampling.py

@@ -227,6 +227,8 @@ def init_bold_mni_trans_wf(template, mem_gb, omp_nthreads,
 
         bold_mni
             BOLD series, resampled to template space
+        bold_mni_ref
+            Reference, contrast-enhanced summary of the BOLD series, resampled to template space
         bold_mask_mni
             BOLD series mask in template space
 
@@ -251,7 +253,7 @@ def init_bold_mni_trans_wf(template, mem_gb, omp_nthreads,
     )
 
     outputnode = pe.Node(
-        niu.IdentityInterface(fields=['bold_mni', 'bold_mask_mni']),
+        niu.IdentityInterface(fields=['bold_mni', 'bold_mni_ref', 'bold_mask_mni']),
         name='outputnode')
 
     def _aslist(in_value):
@@ -298,14 +300,19 @@ def _aslist(in_value):
     merge = pe.Node(Merge(compress=use_compression), name='merge',
                     mem_gb=mem_gb * 3)
 
+    # Generate a reference on the target T1w space
+    gen_final_ref = init_bold_reference_wf(omp_nthreads)
+
     workflow.connect([
         (inputnode, merge_xforms, [('t1_2_mni_forward_transform', 'in1'),
                                    (('itk_bold_to_t1', _aslist), 'in2')]),
         (merge_xforms, bold_to_mni_transform, [('out', 'transforms')]),
         (inputnode, merge, [('name_source', 'header_source')]),
         (inputnode, bold_to_mni_transform, [('bold_split', 'input_image')]),
         (bold_to_mni_transform, merge, [('out_files', 'in_files')]),
+        (merge, gen_final_ref, [('out_file', 'inputnode.bold_file')]),
         (merge, outputnode, [('out_file', 'bold_mni')]),
+        (gen_final_ref, outputnode, [('outputnode.ref_image', 'bold_mni_ref')]),
     ])
 
     if template_out_grid == 'native':