added single volume fmaps

Author: GalKepler

poetry.lock

@@ -10,7 +10,7 @@
 from keprep.workflows.dwi.utils import read_field_from_json
 
 
-def init_eddy_wf(name: str = "eddy_wf") -> pe.Workflow:
+def init_eddy_wf(name: str = "eddy_wf", fieldmap_is_4d: bool = True) -> pe.Workflow:
     """
     Build the SDC and motion correction workflow.
 
@@ -45,7 +45,8 @@ def init_eddy_wf(name: str = "eddy_wf") -> pe.Workflow:
     )
 
     dwi_b0_extractor = init_extract_b0_wf(name="dwi_b0_extractor")
-    fmap_b0_extractor = init_extract_b0_wf(name="fmap_b0_extractor")
+    if fieldmap_is_4d:
+        fmap_b0_extractor = init_extract_b0_wf(name="fmap_b0_extractor")
 
     # node to listify opposite phase encoding directions
     listify_b0 = pe.Node(niu.Merge(2), name="listify_b0")
@@ -87,20 +88,6 @@ def init_eddy_wf(name: str = "eddy_wf") -> pe.Workflow:
                     ("outputnode.dwi_reference", "in1"),
                 ],
             ),
-            (
-                inputnode,
-                fmap_b0_extractor,
-                [
-                    ("fmap_file", "inputnode.dwi_file"),
-                ],
-            ),
-            (
-                fmap_b0_extractor,
-                listify_b0,
-                [
-                    ("outputnode.dwi_reference", "in2"),
-                ],
-            ),
             (
                 listify_b0,
                 prep_pe_pair,
@@ -110,6 +97,37 @@ def init_eddy_wf(name: str = "eddy_wf") -> pe.Workflow:
             ),
         ]
     )
+    if fieldmap_is_4d:
+        workflow.connect(
+            [
+                (
+                    inputnode,
+                    fmap_b0_extractor,
+                    [
+                        ("fmap_file", "inputnode.dwi_file"),
+                    ],
+                ),
+                (
+                    fmap_b0_extractor,
+                    listify_b0,
+                    [
+                        ("outputnode.dwi_reference", "in2"),
+                    ],
+                ),
+            ]
+        )
+    else:
+        workflow.connect(
+            [
+                (
+                    inputnode,
+                    listify_b0,
+                    [
+                        ("fmap_file", "in2"),
+                    ],
+                )
+            ]
+        )
 
     query_pe_dir = pe.Node(
         niu.Function(

src/keprep/workflows/dwi/stages/eddy.py

@@ -21,6 +21,26 @@
 from keprep.workflows.dwi.utils import calculate_denoise_window, read_field_from_json
 
 
+def fieldmap_is_4d(fieldmap_file: str | Path) -> bool:
+    """
+    Check if the fieldmap is 4D.
+
+    Parameters
+    ----------
+    fieldmap_file : Union[str,Path]
+        path to fieldmap file
+
+    Returns
+    -------
+    bool
+        True if the fieldmap is 4D
+    """
+    from nibabel import load
+
+    fieldmap_img = load(str(fieldmap_file))
+    return fieldmap_img.ndim == 4
+
+
 def init_dwi_preproc_wf(dwi_file: str | Path, subject_data: dict):
     """
     Build the dwi preprocessing workflow.
@@ -76,6 +96,10 @@ def init_dwi_preproc_wf(dwi_file: str | Path, subject_data: dict):
     inputnode.inputs.fmap_bvec = Path(layout.get_bvec(fieldmap))
     inputnode.inputs.fmap_bval = Path(layout.get_bval(fieldmap))
     inputnode.inputs.fmap_json = Path(layout.get_nearest(fieldmap, extension="json"))
+
+    # check if fieldmap is 4D
+    fmap_is_4d = fieldmap_is_4d(fieldmap)
+
     outputnode = pe.Node(  # noqa: F841
         niu.IdentityInterface(
             fields=["dwi_preproc", "dwi_reference", "dwi_mask"],
@@ -212,7 +236,7 @@ def init_dwi_preproc_wf(dwi_file: str | Path, subject_data: dict):
         ]
     )
 
-    eddy_wf = init_eddy_wf()
+    eddy_wf = init_eddy_wf(fieldmap_is_4d=fmap_is_4d)
     workflow.connect(
         [
             (inputnode, eddy_wf, [("dwi_json", "inputnode.dwi_json")]),