added GM mask from 5tt

pyproject.toml

@@ -1,7 +1,7 @@
 
 [tool.poetry]
 name = "kepost"
-version = "0.2.10"
+version = "0.2.14"
 description = "Post-processing for dMRI derivatives of the Strauss Neuroplasticity Brain Bank (SNBB)"
 readme = "README.rst"
 authors = ["Gal Kepler <[email protected]>"]

src/kepost/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """Gal Kepler"""
 __email__ = "[email protected]"
-__version__ = "0.2.10"
+__version__ = "0.2.14"

src/kepost/workflows/anatomical/anatomical.py

@@ -21,6 +21,7 @@
     init_gm_cropping_wf,
     init_registration_wf,
 )
+from kepost.workflows.anatomical.procedures.generate_gm import init_gm_from_5tt_wf
 
 
 def init_anatomical_wf(
@@ -160,17 +161,6 @@ def init_anatomical_wf(
 
     workflow.connect(
         [
-            (
-                inputnode,
-                gm_cropping_wf,
-                [
-                    (
-                        "gm_probabilistic_segmentation",
-                        "inputnode.gm_probabilistic_segmentation",
-                    ),
-                    ("probseg_threshold", "inputnode.probseg_threshold"),
-                ],
-            ),
             (
                 registration_wf,
                 gm_cropping_wf,
@@ -240,6 +230,33 @@ def init_anatomical_wf(
         ]
     )
 
+    gm_from_five_tissue = init_gm_from_5tt_wf()
+    workflow.connect(
+        [
+            (
+                five_tissue_type,
+                gm_from_five_tissue,
+                [
+                    ("outputnode.five_tissue_type", "inputnode.five_tissue_type"),
+                ],
+            ),
+            (
+                inputnode,
+                gm_cropping_wf,
+                [
+                    ("probseg_threshold", "inputnode.probseg_threshold"),
+                ],
+            ),
+            (
+                gm_from_five_tissue,
+                gm_cropping_wf,
+                [
+                    ("outputnode.gm_mask", "inputnode.gm_probabilistic_segmentation"),
+                ],
+            ),
+        ]
+    )
+
     derivatives_wf = init_derivatives_wf()
     workflow.connect(
         [

src/kepost/workflows/anatomical/procedures/generate_gm.py

@@ -0,0 +1,146 @@
+from nipype.interfaces import utility as niu
+from nipype.interfaces.fsl import ExtractROI, ImageMaths
+from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
+
+from kepost.interfaces.mrtrix3 import MRConvert
+
+
+def init_gm_from_5tt_wf(name: str = "gm_from_5tt"):
+    """
+    Initialize the gm from 5tt workflow.
+
+    Parameters
+    ----------
+    name : str, optional
+        The name of the workflow, by default "gm_from_5tt"
+
+    Returns
+    -------
+    workflow : nipype.pipeline.engine.Workflow
+        The gm from 5tt workflow.
+    """
+    workflow = Workflow(name=name)
+    inputnode = pe.Node(
+        interface=niu.IdentityInterface(
+            fields=[
+                "five_tissue_type",
+            ]
+        ),
+        name="inputnode",
+    )
+    outputnode = pe.Node(
+        interface=niu.IdentityInterface(
+            fields=[
+                "gm_mask",
+            ]
+        ),
+        name="outputnode",
+    )
+    mrconvert = pe.Node(
+        interface=MRConvert(
+            out_file="five_tissue_type.nii.gz",
+        ),
+        name="mrconvert",
+    )
+    fslroi_cortical_gm = pe.Node(
+        interface=ExtractROI(
+            t_min=0,
+            t_size=1,
+        ),
+        name="fslroi_cortical_gm",
+    )
+    fslroi_subcortical_gm = pe.Node(
+        interface=ExtractROI(
+            t_min=1,
+            t_size=1,
+        ),
+        name="fslroi_subcortical_gm",
+    )
+    fslroi_pathological_gm = pe.Node(
+        interface=ExtractROI(
+            t_min=4,
+            t_size=1,
+        ),
+        name="fslroi_pathological_gm",
+    )
+    fslmaths_cortical_subcortical = pe.Node(
+        interface=ImageMaths(
+            op_string="-add",
+        ),
+        name="fslmaths_cortical_subcortical",
+    )
+    fslmaths_cortical_subcortical_pathological = pe.Node(
+        interface=ImageMaths(
+            op_string="-add",
+        ),
+        name="fslmaths_cortical_subcortical_pathological",
+    )
+    workflow.connect(
+        [
+            (
+                inputnode,
+                mrconvert,
+                [
+                    ("five_tissue_type", "in_file"),
+                ],
+            ),
+            (
+                mrconvert,
+                fslroi_cortical_gm,
+                [
+                    ("out_file", "in_file"),
+                ],
+            ),
+            (
+                mrconvert,
+                fslroi_subcortical_gm,
+                [
+                    ("out_file", "in_file"),
+                ],
+            ),
+            (
+                mrconvert,
+                fslroi_pathological_gm,
+                [
+                    ("out_file", "in_file"),
+                ],
+            ),
+            (
+                fslroi_cortical_gm,
+                fslmaths_cortical_subcortical,
+                [
+                    ("roi_file", "in_file"),
+                ],
+            ),
+            (
+                fslroi_subcortical_gm,
+                fslmaths_cortical_subcortical,
+                [
+                    ("roi_file", "in_file2"),
+                ],
+            ),
+            (
+                fslroi_pathological_gm,
+                fslmaths_cortical_subcortical_pathological,
+                [
+                    ("roi_file", "in_file"),
+                ],
+            ),
+            (
+                fslmaths_cortical_subcortical,
+                fslmaths_cortical_subcortical_pathological,
+                [
+                    ("out_file", "in_file2"),
+                ],
+            ),
+            (
+                fslmaths_cortical_subcortical_pathological,
+                outputnode,
+                [
+                    ("out_file", "gm_mask"),
+                ],
+            ),
+        ]
+    )
+    return workflow