Load T1w-to-standard transform to same space as volumetric BOLD scan

xcp_d/data/transform/tpl-MNI152NLin6Asym_from-MNIInfant_mode-image_xfm.txt

@@ -0,0 +1,5 @@
+#Insight Transform File V1.0
+#Transform 0
+Transform: MatrixOffsetTransformBase_double_3_3
+Parameters:  0.7514471411705017 -0.0022597732022405 -0.0056457491591573 -0.0011661121388897 0.7435653805732727 0.0801302567124367 0.0081897228956223 -0.0277762282639742 0.6979145407676697 0.4968573749065399 -3.0900352001190186 0.6142088770866394
+FixedParameters: 0 0 0

xcp_d/data/transform/tpl-MNI152NLin6Asym_from-MNIInfant_xfm.txt

@@ -0,0 +1,4 @@
+1.330660649  -0.004427136451  0.01025602509  -41.20370054
+-0.003753457765  1.339140797  0.153721562  -68.37553187
+-0.01546533827  -0.05324436952  1.426601839  -22.76900701
+0  0  0  1

xcp_d/tests/test_utils_utils.py

@@ -155,18 +155,18 @@ def test_denoise_with_nilearn(ds001419_data, tmp_path_factory):
 
 def test_list_to_str():
     """Test the list_to_str function."""
-    lst = ["a"]
-    string = utils.list_to_str(lst)
+    string = utils.list_to_str(["a"])
     assert string == "a"
 
-    lst = ["a", "b"]
-    string = utils.list_to_str(lst)
+    string = utils.list_to_str(["a", "b"])
     assert string == "a and b"
 
-    lst = ["a", "b", "c"]
-    string = utils.list_to_str(lst)
+    string = utils.list_to_str(["a", "b", "c"])
     assert string == "a, b, and c"
 
+    with pytest.raises(ValueError, match="Zero-length list provided."):
+        utils.list_to_str([])
+
 
 def test_get_bold2std_and_t1w_xfms(ds001419_data):
     """Test get_bold2std_and_t1w_xfms."""
@@ -331,30 +331,56 @@ def test_get_std2bold_xfms(ds001419_data):
     """
     bold_file_nlin2009c = ds001419_data["nifti_file"]
 
+    # MNI152NLin6Asym --> MNI152NLin2009cAsym
+    xforms_to_mni = utils.get_std2bold_xfms(bold_file_nlin2009c, inverted=False)
+    assert len(xforms_to_mni) == 1
+
+    # MNI152NLin6Asym --> MNI152NLin6Asym
+    bold_file_nlin6asym = bold_file_nlin2009c.replace(
+        "space-MNI152NLin2009cAsym_",
+        "space-MNI152NLin6Asym_",
+    )
+    xforms_to_mni = utils.get_std2bold_xfms(bold_file_nlin6asym, inverted=False)
+    assert len(xforms_to_mni) == 1
+
+    # MNI152NLin6Asym --> MNIInfant
+    bold_file_infant = bold_file_nlin2009c.replace(
+        "space-MNI152NLin2009cAsym_",
+        "space-MNIInfant_cohort-1_",
+    )
+    xforms_to_mni = utils.get_std2bold_xfms(bold_file_infant, inverted=False)
+    assert len(xforms_to_mni) == 2
+
+    # MNI152NLin6Asym --> tofail
+    bold_file_tofail = bold_file_nlin2009c.replace("space-MNI152NLin2009cAsym_", "space-tofail_")
+    with pytest.raises(ValueError, match="Space 'tofail'"):
+        utils.get_std2bold_xfms(bold_file_tofail, inverted=False)
+
+    # Inverted version
     # MNI152NLin2009cAsym --> MNI152NLin6Asym
-    xforms_to_mni = utils.get_std2bold_xfms(bold_file_nlin2009c)
+    xforms_to_mni = utils.get_std2bold_xfms(bold_file_nlin2009c, inverted=True)
     assert len(xforms_to_mni) == 1
 
     # MNI152NLin6Asym --> MNI152NLin6Asym
     bold_file_nlin6asym = bold_file_nlin2009c.replace(
         "space-MNI152NLin2009cAsym_",
         "space-MNI152NLin6Asym_",
     )
-    xforms_to_mni = utils.get_std2bold_xfms(bold_file_nlin6asym)
+    xforms_to_mni = utils.get_std2bold_xfms(bold_file_nlin6asym, inverted=True)
     assert len(xforms_to_mni) == 1
 
     # MNIInfant --> MNI152NLin6Asym
     bold_file_infant = bold_file_nlin2009c.replace(
         "space-MNI152NLin2009cAsym_",
         "space-MNIInfant_cohort-1_",
     )
-    xforms_to_mni = utils.get_std2bold_xfms(bold_file_infant)
+    xforms_to_mni = utils.get_std2bold_xfms(bold_file_infant, inverted=True)
     assert len(xforms_to_mni) == 2
 
     # tofail --> MNI152NLin6Asym
     bold_file_tofail = bold_file_nlin2009c.replace("space-MNI152NLin2009cAsym_", "space-tofail_")
     with pytest.raises(ValueError, match="Space 'tofail'"):
-        utils.get_std2bold_xfms(bold_file_tofail)
+        utils.get_std2bold_xfms(bold_file_tofail, inverted=True)
 
 
 def test_fwhm2sigma():

xcp_d/utils/bids.py

@@ -32,8 +32,8 @@
     "nibabies": {
         "cifti": ["fsLR"],
         "nifti": [
-            "MNIInfant",
             "MNI152NLin6Asym",
+            "MNIInfant",
             "MNI152NLin2009cAsym",
         ],
     },

xcp_d/utils/utils.py

@@ -143,7 +143,7 @@ def get_bold2std_and_t1w_xfms(bold_file, template_to_anat_xfm, anat_to_native_xf
     return xforms_to_MNI, xforms_to_MNI_invert, xforms_to_T1w, xforms_to_T1w_invert
 
 
-def get_std2bold_xfms(bold_file):
+def get_std2bold_xfms(bold_file, inverted=False):
     """Obtain transforms to warp atlases from MNI152NLin6Asym to the same template as the BOLD.
 
     Since ANTSApplyTransforms takes in the transform files as a stack,
@@ -155,6 +155,9 @@ def get_std2bold_xfms(bold_file):
     ----------
     bold_file : :obj:`str`
         The preprocessed BOLD file.
+    inverted : :obj:`bool`, optional
+        If False (default), transforms from MNI152NLin6Asym will be returned.
+        If True, transforms *to* MNI152NLin6Asym will be returned.
 
     Returns
     -------
@@ -168,9 +171,7 @@ def get_std2bold_xfms(bold_file):
     - to resample dseg in init_postprocess_nifti_wf for QCReport
     - to warp atlases to the same space as the BOLD data in init_functional_connectivity_nifti_wf
     - to resample dseg to BOLD space for the executive summary plots
-
-    Does not include inversion flag output because there is no need (yet).
-    Can easily be added in the future.
+    - to warp any BOLD images that will be overlaid on anatomical images to MNI152NLin6Asym
     """
     import os
 
@@ -192,30 +193,56 @@ def get_std2bold_xfms(bold_file):
             **{"from": "MNI152NLin6Asym"},
         ),
     )
+    MNI152NLin2009cAsym_to_MNI152NLin6Asym = str(
+        get_template(
+            template="MNI152NLin6Asym",
+            mode="image",
+            suffix="xfm",
+            extension=".h5",
+            **{"from": "MNI152NLin2009cAsym"},
+        ),
+    )
 
     # Find the appropriate transform(s)
     if bold_space == "MNI152NLin6Asym":
         # NLin6 --> NLin6 (identity)
         transform_list = ["identity"]
 
     elif bold_space == "MNI152NLin2009cAsym":
-        # NLin6 --> NLin2009c
-        transform_list = [MNI152NLin6Asym_to_MNI152NLin2009cAsym]
+        if inverted:
+            # NLin2009c --> NLin6
+            transform_list = [MNI152NLin2009cAsym_to_MNI152NLin6Asym]
+
+        else:
+            # NLin6 --> NLin2009c
+            transform_list = [MNI152NLin6Asym_to_MNI152NLin2009cAsym]
 
     elif bold_space == "MNIInfant":
-        # NLin6 --> NLin2009c --> MNIInfant
-        MNI152NLin2009cAsym_to_MNI152Infant = pkgrf(
-            "xcp_d",
-            "data/transform/tpl-MNIInfant_from-MNI152NLin2009cAsym_mode-image_xfm.h5",
-        )
-        transform_list = [
-            MNI152NLin2009cAsym_to_MNI152Infant,
-            MNI152NLin6Asym_to_MNI152NLin2009cAsym,
-        ]
+        if inverted:
+            # MNIInfant --> NLin2009c --> NLin6
+            # The available MNIInfant --> MNI152* transforms seem to be of poor quality
+            MNI152Infant_to_MNI152NLin2009cAsym = pkgrf(
+                "xcp_d",
+                "data/transform/tpl-MNI152NLin2009cAsym_from-MNIInfant_mode-image_xfm.h5",
+            )
+            transform_list = [
+                MNI152NLin2009cAsym_to_MNI152NLin6Asym,
+                MNI152Infant_to_MNI152NLin2009cAsym,
+            ]
+
+        else:
+            # NLin6 --> NLin2009c --> MNIInfant
+            MNI152NLin2009cAsym_to_MNI152Infant = pkgrf(
+                "xcp_d",
+                "data/transform/tpl-MNIInfant_from-MNI152NLin2009cAsym_mode-image_xfm.h5",
+            )
+            transform_list = [
+                MNI152NLin2009cAsym_to_MNI152Infant,
+                MNI152NLin6Asym_to_MNI152NLin2009cAsym,
+            ]
 
     else:
-        file_base = os.path.basename(bold_file)
-        raise ValueError(f"Space '{bold_space}' in {file_base} not supported.")
+        raise ValueError(f"Space '{bold_space}' in {os.path.basename(bold_file)} not supported.")
 
     return transform_list
 

xcp_d/workflows/base.py

@@ -670,9 +670,9 @@ def init_subject_wf(
 
         for j_run, bold_file in enumerate(task_files):
             run_data = collect_run_data(
-                layout,
-                input_type,
-                bold_file,
+                layout=layout,
+                input_type=input_type,
+                bold_file=bold_file,
                 cifti=cifti,
                 primary_anat=primary_anat,
             )