Merge pull request #271 from madisoth/enh/t2-vol-out

ENH: Add preprocessed T2w volume to outputs

Author: mgxd

.circleci/bcp_anat_outputs.txt

@@ -47,3 +47,4 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.nii.gz

.circleci/bcp_full_outputs.txt

@@ -47,6 +47,7 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.nii.gz
 sub-01/ses-1mo/fmap
 sub-01/ses-1mo/fmap/sub-01_ses-1mo_run-001_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
 sub-01/ses-1mo/fmap/sub-01_ses-1mo_run-001_fmapid-auto00000_desc-epi_fieldmap.nii.gz

nibabies/workflows/anatomical/base.py

@@ -77,6 +77,9 @@ def init_infant_anat_wf(
     """
     from nipype.interfaces.ants.base import Info as ANTsInfo
     from niworkflows.engine.workflows import LiterateWorkflow as Workflow
+    from sdcflows.workflows.ancillary import (
+        init_brainextraction_wf as init_sdc_brain_extraction_wf,
+    )
 
     from ...utils.misc import fix_multi_source_name
     from .brain_extraction import (
@@ -214,25 +217,26 @@ def init_infant_anat_wf(
     if precomp_mask:
         precomp_mask_wf = init_precomputed_mask_wf(omp_nthreads=omp_nthreads)
         precomp_mask_wf.inputs.inputnode.t1w_mask = precomp_mask
-
-    else:
-        brain_extraction_wf = init_infant_brain_extraction_wf(
-            age_months=age_months,
-            ants_affine_init=ants_affine_init,
-            skull_strip_template=skull_strip_template.space,
-            template_specs=skull_strip_template.spec,
-            omp_nthreads=omp_nthreads,
-            sloppy=sloppy,
-            debug="registration" in config.execution.debug,
-        )
-        coregistration_wf = init_coregistration_wf(
-            omp_nthreads=omp_nthreads,
-            sloppy=sloppy,
-            debug="registration" in config.execution.debug,
-        )
-        coreg_report_wf = init_coreg_report_wf(
-            output_dir=output_dir,
+        sdc_brain_extraction_wf = init_sdc_brain_extraction_wf(
+            name="sdc_brain_extraction_wf",
         )
+    brain_extraction_wf = init_infant_brain_extraction_wf(
+        age_months=age_months,
+        ants_affine_init=ants_affine_init,
+        skull_strip_template=skull_strip_template.space,
+        template_specs=skull_strip_template.spec,
+        omp_nthreads=omp_nthreads,
+        sloppy=sloppy,
+        debug="registration" in config.execution.debug,
+    )
+    coregistration_wf = init_coregistration_wf(
+        omp_nthreads=omp_nthreads,
+        sloppy=sloppy,
+        debug="registration" in config.execution.debug,
+    )
+    coreg_report_wf = init_coreg_report_wf(
+        output_dir=output_dir,
+    )
     t1w_preproc_wf = precomp_mask_wf if precomp_mask else coregistration_wf
 
     # Segmentation - initial implementation should be simple: JLF
@@ -285,6 +289,9 @@ def init_infant_anat_wf(
             ("outputnode.t1w_mask", "inputnode.t1w_mask"),
             ("outputnode.t1w_preproc", "inputnode.t1w_preproc"),
         ]),
+        (coregistration_wf, anat_derivatives_wf, [
+            ("outputnode.t2w_preproc", "inputnode.t2w_preproc")
+         ]),
         (t1w_preproc_wf, outputnode, [
             ("outputnode.t1w_preproc", "anat_preproc"),
             ("outputnode.t1w_brain", "anat_brain"),
@@ -296,36 +303,50 @@ def init_infant_anat_wf(
         wf.connect([
             (t1w_preproc_wf, anat_seg_wf, [("outputnode.t1w_brain", "inputnode.anat_brain")]),
         ])
-
+    wf.connect([
+        (inputnode, t2w_template_wf, [("t2w", "inputnode.in_files")]),
+    ])
     if precomp_mask:
         wf.connect([
             (t1w_template_wf, precomp_mask_wf, [
                 ("outputnode.out_file", "inputnode.t1w"),
             ]),
+            (t2w_template_wf, sdc_brain_extraction_wf, [
+                ("outputnode.out_file", "inputnode.in_file"),
+            ]),
+            (sdc_brain_extraction_wf, coregistration_wf, [
+                ("outputnode.out_file", "inputnode.in_t2w_preproc"),
+                ("outputnode.out_mask", "inputnode.in_mask"),
+                ("outputnode.out_probseg", "inputnode.in_probmap"),
+            ]),
         ])
     else:
         wf.connect([
-            (inputnode, t2w_template_wf, [("t2w", "inputnode.in_files")]),
             (t2w_template_wf, brain_extraction_wf, [
                 ("outputnode.out_file", "inputnode.in_t2w"),
             ]),
-            (t1w_template_wf, coregistration_wf, [
-                ("outputnode.out_file", "inputnode.in_t1w"),
-            ]),
             (brain_extraction_wf, coregistration_wf, [
                 ("outputnode.t2w_preproc", "inputnode.in_t2w_preproc"),
                 ("outputnode.out_mask", "inputnode.in_mask"),
                 ("outputnode.out_probmap", "inputnode.in_probmap"),
             ]),
-            (inputnode, coreg_report_wf, [
-                ("t1w", "inputnode.source_file"),
-            ]),
-            (t1w_preproc_wf, coreg_report_wf, [
-                ("outputnode.t1w_preproc", "inputnode.t1w_preproc"),
-                ("outputnode.t2w_preproc", "inputnode.t2w_preproc"),
-                ("outputnode.t1w_mask", "inputnode.in_mask"),
-            ]),
         ])
+    wf.connect([
+        (t1w_template_wf, coregistration_wf, [
+            ("outputnode.out_file", "inputnode.in_t1w"),
+        ]),
+
+        (inputnode, coreg_report_wf, [
+            ("t1w", "inputnode.source_file"),
+        ]),
+        (t1w_preproc_wf, coreg_report_wf, [
+            ("outputnode.t1w_preproc", "inputnode.t1w_preproc"),
+            ("outputnode.t1w_mask", "inputnode.in_mask"),
+        ]),
+        (coregistration_wf, coreg_report_wf, [
+            ("outputnode.t2w_preproc", "inputnode.t2w_preproc")
+        ]),
+    ])
 
     wf.connect([
         # reports
@@ -350,6 +371,9 @@ def init_infant_anat_wf(
             ("outputnode.valid_list", "inputnode.source_files"),
             ("outputnode.realign_xfms", "inputnode.t1w_ref_xfms"),
         ]),
+        (t2w_template_wf, anat_derivatives_wf, [
+            ("outputnode.valid_list", "inputnode.t2w_source_files"),
+        ]),
         (anat_norm_wf, anat_derivatives_wf, [
             ("outputnode.template", "inputnode.template"),
             ("outputnode.anat2std_xfm", "inputnode.anat2std_xfm"),

nibabies/workflows/anatomical/outputs.py

@@ -310,6 +310,10 @@ def init_anat_derivatives_wf(
         FreeSurfer's aseg segmentation, in native T1w space
     t1w_fs_aparc
         FreeSurfer's aparc+aseg segmentation, in native T1w space
+    t2w_source_files
+        List of input T2w images
+    t2w_preproc
+        The T2w image in T1w space.
     """
     from niworkflows.interfaces.nibabel import ApplyMask
     from niworkflows.interfaces.utility import KeySelect
@@ -341,6 +345,8 @@ def init_anat_derivatives_wf(
                 "morphometrics",
                 "t1w_fs_aseg",
                 "t1w_fs_aparc",
+                "t2w_source_files",
+                "t2w_preproc",
             ]
         ),
         name="inputnode",
@@ -369,6 +375,14 @@ def init_anat_derivatives_wf(
         run_without_submitting=True,
     )
 
+    ds_t2w_preproc = pe.Node(
+        DerivativesDataSink(
+            data_dtype="i2", base_directory=output_dir, space="T1w", desc="preproc", compress=True
+        ),
+        name="ds_t2w_preproc",
+        run_without_submitting=True,
+    )
+
     ds_t1w_tpms = pe.Node(
         DerivativesDataSink(base_directory=output_dir, suffix="probseg", compress=True),
         name="ds_t1w_tpms",
@@ -381,6 +395,8 @@ def init_anat_derivatives_wf(
         (inputnode, raw_sources, [('source_files', 'in_files')]),
         (inputnode, ds_t1w_preproc, [('t1w_preproc', 'in_file'),
                                      ('source_files', 'source_file')]),
+        (inputnode, ds_t2w_preproc, [('t2w_preproc', 'in_file'),
+                                     ('t2w_source_files', 'source_file')]),
         (inputnode, ds_t1w_mask, [('t1w_mask', 'in_file'),
                                   ('source_files', 'source_file')]),
         (inputnode, ds_t1w_tpms, [('t1w_tpms', 'in_file'),