Lots of changes.

aslprep/interfaces/cbf.py

@@ -38,7 +38,11 @@
 class _RefineMaskInputSpec(BaseInterfaceInputSpec):
     t1w_mask = File(exists=True, mandatory=True, desc="t1 mask")
     asl_mask = File(exists=True, mandatory=True, desct="asl mask")
-    transforms = File(exists=True, mandatory=True, desc="transfom")
+    aslref2anat_xfm = File(
+        exists=True,
+        mandatory=True,
+        desc="Transform from reference to anatomical space.",
+    )
 
 
 class _RefineMaskOutputSpec(TraitedSpec):
@@ -67,7 +71,7 @@ def _run_interface(self, runtime):
         refine_ref_mask(
             t1w_mask=self.inputs.t1w_mask,
             ref_asl_mask=self.inputs.asl_mask,
-            t12ref_transform=self.inputs.transforms,
+            aslref2anat_xfm=self.inputs.aslref2anat_xfm,
             tmp_mask=self._results["out_tmp"],
             refined_mask=self._results["out_mask"],
         )
@@ -984,7 +988,7 @@ def regmotoasl(asl, m0file):
     return flt_results.outputs.out_file
 
 
-def refine_ref_mask(t1w_mask, ref_asl_mask, t12ref_transform, tmp_mask, refined_mask):
+def refine_ref_mask(t1w_mask, ref_asl_mask, aslref2anat_xfm, tmp_mask, refined_mask):
     """Warp T1w mask to ASL space, then use it to mask the ASL mask.
 
     TODO: This should not be a function. It uses interfaces, so it should be a workflow.
@@ -995,7 +999,8 @@ def refine_ref_mask(t1w_mask, ref_asl_mask, t12ref_transform, tmp_mask, refined_
         input_image=t1w_mask,
         interpolation="NearestNeighbor",
         reference_image=ref_asl_mask,
-        transforms=[t12ref_transform],
+        transforms=[aslref2anat_xfm],
+        invert_transform_flags=[True],
         input_image_type=3,
         output_image=tmp_mask,
     )

aslprep/workflows/asl/base.py

@@ -402,13 +402,13 @@ def init_asl_preproc_wf(
         ]),
         (asl_fit_wf, cbf_wf, [
             ("outputnode.asl_mask", "inputnode.asl_mask"),
+            ("outputnode.aslref2anat_xfm", "inputnode.aslref2anat_xfm"),
+        ]),
+        (asl_native_wf, cbf_wf, [
+            ("outputnode.asl_native", "inputnode.asl_file"),
             ("outputnode.aslcontext", "inputnode.aslcontext"),
-            ("outputnode.m0scan", "inputnode.m0scan"),
-            # XXX: doesn't exist!
-            ("outputnode.anat_to_aslref_xfm", "inputnode.anat_to_aslref_xfm"),
-            ("outputnode.aslref_to_anat_xfm", "inputnode.aslref_to_anat_xfm"),
+            ("outputnode.m0scan_native", "inputnode.m0scan"),
         ]),
-        (asl_native_wf, cbf_wf, [("outputnode.asl_native", "inputnode.asl_file")]),
     ])
     # fmt:on
 
@@ -517,8 +517,7 @@ def init_asl_preproc_wf(
             ]),
             (asl_fit_wf, parcellate_cbf_wf, [
                 ("outputnode.asl_mask", "inputnode.asl_mask"),
-                # XXX: doesn't exist!
-                ("outputnode.anat_to_aslref_xfm", "inputnode.anat_to_aslref_xfm"),
+                ("outputnode.aslref2anat_xfm", "inputnode.aslref2anat_xfm"),
             ]),
         ])
         # fmt:on
@@ -692,7 +691,7 @@ def init_asl_preproc_wf(
         ]),
         (asl_fit_wf, cbf_qc_wf, [
             ("outputnode.asl_mask", "inputnode.asl_mask"),
-            ("outputnode.anat_to_aslref_xfm", "inputnode.anat_to_aslref_xfm"),
+            ("outputnode.aslref2anat_xfm", "inputnode.aslref2anat_xfm"),
             ("outputnode.rmsd_file", "inputnode.rmsd_file"),
         ]),
         (asl_confounds_wf, cbf_qc_wf, [("outputnode.confounds_file", "inputnode.confounds_file")]),
@@ -724,8 +723,7 @@ def init_asl_preproc_wf(
         ]),
         (asl_fit_wf, plot_cbf_wf, [
             ("outputnode.coreg_aslref", "inputnode.aslref"),
-            # XXX: doesn't exist
-            ("outputnode.anat_to_aslref_xfm", "inputnode.anat_to_aslref_xfm"),
+            ("outputnode.aslref2anat_xfm", "inputnode.aslref2anat_xfm"),
             # XXX: Used to use the one from refine_mask
             ("inputnode.asl_mask", "inputnode.asl_mask"),
         ]),

aslprep/workflows/asl/cbf.py

@@ -95,9 +95,7 @@ def init_cbf_wf(
         t1w probability maps
     t1w_mask
         t1w mask Nifti
-    anat_to_aslref_xfm
-        t1w to asl transformation file
-    aslref_to_anat_xfm
+    aslref2anat_xfm
         asl to t1w transformation file
 
     Outputs
@@ -228,9 +226,8 @@ def init_cbf_wf(
                 "asl_mask",
                 "t1w_tpms",
                 "t1w_mask",
-                "anat_to_aslref_xfm",
-                "aslref_to_anat_xfm",
-            ]
+                "aslref2anat_xfm",
+            ],
         ),
         name="inputnode",
     )
@@ -268,7 +265,7 @@ def init_cbf_wf(
         (inputnode, refine_mask, [
             ("t1w_mask", "t1w_mask"),
             ("asl_mask", "asl_mask"),
-            ("anat_to_aslref_xfm", "transforms"),
+            ("aslref2anat_xfm", "aslref2anat_xfm"),
         ]),
     ])
     # fmt:on
@@ -289,7 +286,11 @@ def _getfiledir(file):
         return os.path.dirname(file)
 
     gm_tfm = pe.Node(
-        ApplyTransforms(interpolation="NearestNeighbor", float=True),
+        ApplyTransforms(
+            interpolation="NearestNeighbor",
+            float=True,
+            invert_transform_flags=[True],
+        ),
         name="gm_tfm",
         mem_gb=0.1,
     )
@@ -298,14 +299,18 @@ def _getfiledir(file):
     workflow.connect([
         (inputnode, gm_tfm, [
             ("asl_mask", "reference_image"),
-            ("anat_to_aslref_xfm", "transforms"),
+            ("aslref2anat_xfm", "transforms"),
             (("t1w_tpms", _pick_gm), "input_image"),
         ]),
     ])
     # fmt:on
 
     wm_tfm = pe.Node(
-        ApplyTransforms(interpolation="NearestNeighbor", float=True),
+        ApplyTransforms(
+            interpolation="NearestNeighbor",
+            float=True,
+            invert_transform_flags=[True],
+        ),
         name="wm_tfm",
         mem_gb=0.1,
     )
@@ -314,14 +319,18 @@ def _getfiledir(file):
     workflow.connect([
         (inputnode, wm_tfm, [
             ("asl_mask", "reference_image"),
-            ("anat_to_aslref_xfm", "transforms"),
+            ("aslref2anat_xfm", "transforms"),
             (("t1w_tpms", _pick_wm), "input_image"),
         ]),
     ])
     # fmt:on
 
     csf_tfm = pe.Node(
-        ApplyTransforms(interpolation="NearestNeighbor", float=True),
+        ApplyTransforms(
+            interpolation="NearestNeighbor",
+            float=True,
+            invert_transform_flags=[True],
+        ),
         name="csf_tfm",
         mem_gb=0.1,
     )
@@ -330,7 +339,7 @@ def _getfiledir(file):
     workflow.connect([
         (inputnode, csf_tfm, [
             ("asl_mask", "reference_image"),
-            ("anat_to_aslref_xfm", "transforms"),
+            ("aslref2anat_xfm", "transforms"),
             (("t1w_tpms", _pick_csf), "input_image"),
         ]),
     ])
@@ -563,8 +572,7 @@ def init_compute_cbf_ge_wf(
                 "asl_mask",
                 "t1w_tpms",
                 "t1w_mask",
-                "anat_to_aslref_xfm",
-                "aslref_to_anat_xfm",
+                "aslref2anat_xfm",
                 "m0_file",
                 "m0tr",
             ]
@@ -609,7 +617,11 @@ def _getfiledir(file):
     # convert tmps to asl_space
     # extract probability maps
     csf_tfm = pe.Node(
-        ApplyTransforms(interpolation="NearestNeighbor", float=True),
+        ApplyTransforms(
+            interpolation="NearestNeighbor",
+            float=True,
+            invert_transform_flags=[True],
+        ),
         name="csf_tfm",
         mem_gb=0.1,
     )
@@ -618,14 +630,18 @@ def _getfiledir(file):
     workflow.connect([
         (inputnode, csf_tfm, [
             ("asl_mask", "reference_image"),
-            ("anat_to_aslref_xfm", "transforms"),
+            ("aslref2anat_xfm", "transforms"),
             (("t1w_tpms", _pick_csf), "input_image"),
         ]),
     ])
     # fmt:on
 
     wm_tfm = pe.Node(
-        ApplyTransforms(interpolation="NearestNeighbor", float=True),
+        ApplyTransforms(
+            interpolation="NearestNeighbor",
+            float=True,
+            invert_transform_flags=[True],
+        ),
         name="wm_tfm",
         mem_gb=0.1,
     )
@@ -634,14 +650,18 @@ def _getfiledir(file):
     workflow.connect([
         (inputnode, wm_tfm, [
             ("asl_mask", "reference_image"),
-            ("anat_to_aslref_xfm", "transforms"),
+            ("aslref2anat_xfm", "transforms"),
             (("t1w_tpms", _pick_wm), "input_image"),
         ]),
     ])
     # fmt:on
 
     gm_tfm = pe.Node(
-        ApplyTransforms(interpolation="NearestNeighbor", float=True),
+        ApplyTransforms(
+            interpolation="NearestNeighbor",
+            float=True,
+            invert_transform_flags=[True],
+        ),
         name="gm_tfm",
         mem_gb=0.1,
     )
@@ -650,7 +670,7 @@ def _getfiledir(file):
     workflow.connect([
         (inputnode, gm_tfm, [
             ("asl_mask", "reference_image"),
-            ("anat_to_aslref_xfm", "transforms"),
+            ("aslref2anat_xfm", "transforms"),
             (("t1w_tpms", _pick_gm), "input_image"),
         ]),
     ])
@@ -679,7 +699,7 @@ def _getfiledir(file):
         (inputnode, refine_mask, [
             ("t1w_mask", "t1w_mask"),
             ("asl_mask", "asl_mask"),
-            ("anat_to_aslref_xfm", "transforms"),
+            ("aslref2anat_xfm", "aslref2anat_xfm"),
         ]),
     ])
     # fmt:on
@@ -918,7 +938,7 @@ def init_parcellate_cbf_wf(
     mean_cbf_basil : Undefined or str
     mean_cbf_gm_basil : Undefined or str
     asl_mask : str
-    anat_to_aslref_xfm : str
+    aslref2anat_xfm : str
     MNI152NLin2009cAsym_to_anat_xfm : str
         The transform from MNI152NLin2009cAsym to the subject's anatomical space.
 
@@ -965,7 +985,7 @@ def init_parcellate_cbf_wf(
                 "mean_cbf_basil",
                 "mean_cbf_gm_basil",
                 "asl_mask",
-                "anat_to_aslref_xfm",
+                "aslref2anat_xfm",
                 "MNI152NLin2009cAsym_to_anat_xfm",
             ],
         ),
@@ -1030,7 +1050,7 @@ def init_parcellate_cbf_wf(
     workflow.connect([
         (inputnode, merge_xforms, [
             ("MNI152NLin2009cAsym_to_anat_xfm", "in2"),
-            ("anat_to_aslref_xfm", "in3"),
+            ("aslref2anat_xfm", "in3"),
         ]),
     ])
     # fmt:on
@@ -1041,6 +1061,7 @@ def init_parcellate_cbf_wf(
             interpolation="GenericLabel",
             input_image_type=3,
             dimension=3,
+            invert_transform_flags=[False, False, True],
         ),
         name="warp_atlases_to_asl_space",
         iterfield=["input_image"],

aslprep/workflows/asl/confounds.py

@@ -74,7 +74,7 @@ def init_asl_confounds_wf(
         Mask of the skull-stripped template image
     t1w_tpms
         List of tissue probability maps in T1w space
-    anat_to_aslref_xfm
+    aslref2anat_xfm
         Affine matrix that maps the T1w space into alignment with
         the native asl space
 
@@ -110,7 +110,7 @@ def init_asl_confounds_wf(
                 "skip_vols",
                 "t1w_mask",
                 "t1w_tpms",
-                "anat_to_aslref_xfm",
+                "aslref2anat_xfm",
             ],
         ),
         name="inputnode",
@@ -184,7 +184,7 @@ def init_asl_confounds_wf(
 
     # Project T1w mask into BOLD space and merge with BOLD brainmask
     t1w_mask_tfm = pe.Node(
-        ApplyTransforms(interpolation="MultiLabel"),
+        ApplyTransforms(interpolation="MultiLabel", invert_transform_flags=[True]),
         name="t1w_mask_tfm",
     )
     union_mask = pe.Node(niu.Function(function=_binary_union), name="union_mask")
@@ -199,7 +199,7 @@ def init_asl_confounds_wf(
         (inputnode, t1w_mask_tfm, [
             ("t1w_mask", "input_image"),
             ("asl_mask", "reference_image"),
-            ("anat_to_aslref_xfm", "transforms"),
+            ("aslref2anat_xfm", "transforms"),
         ]),
         (inputnode, union_mask, [("asl_mask", "mask1")]),
         (t1w_mask_tfm, union_mask, [("output_image", "mask2")]),
@@ -223,15 +223,15 @@ def init_asl_confounds_wf(
 
     # Resample probseg maps in BOLD space via T1w-to-BOLD transform
     acc_msk_tfm = pe.MapNode(
-        ApplyTransforms(interpolation="Gaussian"),
+        ApplyTransforms(interpolation="Gaussian", invert_transform_flags=[True]),
         iterfield=["input_image"],
         name="acc_msk_tfm",
         mem_gb=0.1,
     )
     # fmt:off
     workflow.connect([
         (inputnode, acc_msk_tfm, [
-            ("anat_to_aslref_xfm", "transforms"),
+            ("aslref2anat_xfm", "transforms"),
             ("asl_mask", "reference_image"),
         ]),
         (acc_masks, acc_msk_tfm, [("out_masks", "input_image")]),

aslprep/workflows/asl/ge_utils.py

@@ -184,7 +184,7 @@ def init_asl_reg_ge_wf(
         name="inputnode",
     )
     outputnode = pe.Node(
-        niu.IdentityInterface(fields=["aslref_to_anat_xfm", "anat_to_aslref_xfm", "fallback"]),
+        niu.IdentityInterface(fields=["aslref2anat_xfm", "anat2aslref_xfm", "fallback"]),
         name="outputnode",
     )
 
@@ -203,8 +203,8 @@ def init_asl_reg_ge_wf(
             ("t1w_brain", "inputnode.t1w_brain"),
         ]),
         (bbr_wf, outputnode, [
-            ("outputnode.aslref_to_anat_xfm", "aslref_to_anat_xfm"),
-            ("outputnode.anat_to_aslref_xfm", "anat_to_aslref_xfm"),
+            ("outputnode.aslref2anat_xfm", "aslref2anat_xfm"),
+            ("outputnode.anat2aslref_xfm", "anat2aslref_xfm"),
             ("outputnode.fallback", "fallback"),
         ]),
     ])