docs/changes/latest.inc

@@ -54,6 +54,9 @@ Bugs
 
 - Fix ``junifer run`` to respect preprocess step specified in the pipeline (:gh:`159` by `Synchon Mandal`_).
 
+- Fix :class:`junifer.markers.AmplitudeLowFrequencyFluctuationParcels`, :class:`junifer.markers.AmplitudeLowFrequencyFluctuationSpheres`
+  :class:`junifer.markers.ReHoSpheres` and :class:`junifer.markers.ReHoParcels` pass the ``extra_input`` parameter (:gh:`187` by `Fede Raimondo`_).
+
 API changes
 ~~~~~~~~~~~
 

junifer/markers/falff/falff_base.py

@@ -61,8 +61,8 @@ class AmplitudeLowFrequencyFluctuationBase(BaseMarker):
         use_afni: Optional[bool] = None,
         name: Optional[str] = None,
     ) -> None:
-        if highpass <= 0:
-            raise_error("Highpass must be positive")
+        if highpass < 0:
+            raise_error("Highpass must be positive or 0")
         if lowpass <= 0:
             raise_error("Lowpass must be positive")
         if highpass >= lowpass:
@@ -160,18 +160,25 @@ class AmplitudeLowFrequencyFluctuationBase(BaseMarker):
             "path": None,
         }
 
-        out = self._postprocess(post_input)
+        out = self._postprocess(post_input, extra_input=extra_input)
 
         return out
 
     @abstractmethod
-    def _postprocess(self, input: Dict) -> Dict:
+    def _postprocess(
+        self, input: Dict, extra_input: Optional[Dict] = None
+    ) -> Dict:
         """Postprocess the output of the estimator.
 
         Parameters
         ----------
         input : dict
             The output of the estimator. It must have the following
+        extra_input : dict, optional
+            The other fields in the pipeline data object. Useful for accessing
+            other data kind that needs to be used in the computation. For
+            example, the functional connectivity markers can make use of the
+            confounds if available (default None).
         """
         raise_error(
             "_postprocess must be implemented", klass=NotImplementedError

junifer/markers/falff/falff_parcels.py

@@ -26,7 +26,8 @@ class AmplitudeLowFrequencyFluctuationParcels(
     fractional : bool
         Whether to compute fractional ALFF.
     highpass : positive float, optional
-        The highpass cutoff frequency for the bandpass filter (default 0.01).
+        The highpass cutoff frequency for the bandpass filter. If 0,
+        it will not apply a highpass filter (default 0.01).
     lowpass : positive float, optional
         The lowpass cutoff frequency for the bandpass filter (default 0.1).
     tr : positive float, optional
@@ -88,7 +89,9 @@ class AmplitudeLowFrequencyFluctuationParcels(
             use_afni=use_afni,
         )
 
-    def _postprocess(self, input: Dict) -> Dict:
+    def _postprocess(
+        self, input: Dict, extra_input: Optional[Dict] = None
+    ) -> Dict:
         """Compute ALFF and fALFF.
 
         Parameters
@@ -121,6 +124,6 @@ class AmplitudeLowFrequencyFluctuationParcels(
         )
 
         # get the 2D timeseries after parcel aggregation
-        out = pa.compute(input)
+        out = pa.compute(input, extra_input=extra_input)
 
         return out

junifer/markers/falff/falff_spheres.py

@@ -30,7 +30,8 @@ class AmplitudeLowFrequencyFluctuationSpheres(
     fractional : bool
         Whether to compute fractional ALFF.
     highpass : positive float, optional
-        The highpass cutoff frequency for the bandpass filter (default 0.01).
+        The highpass cutoff frequency for the bandpass filter. If 0,
+        it will not apply a highpass filter (default 0.01).
     lowpass : positive float, optional
         The lowpass cutoff frequency for the bandpass filter (default 0.1).
     tr : positive float, optional
@@ -94,7 +95,9 @@ class AmplitudeLowFrequencyFluctuationSpheres(
             use_afni=use_afni,
         )
 
-    def _postprocess(self, input: Dict) -> Dict:
+    def _postprocess(
+        self, input: Dict, extra_input: Optional[Dict] = None
+    ) -> Dict:
         """Compute ALFF and fALFF.
 
         Parameters
@@ -127,7 +130,7 @@ class AmplitudeLowFrequencyFluctuationSpheres(
             on="fALFF",
         )
 
-        # get the 2D timeseries after parcel aggregation
-        out = pa.compute(input)
+        # get the 2D timeseries after sphere aggregation
+        out = pa.compute(input, extra_input=extra_input)
 
         return out

junifer/markers/reho/reho_parcels.py

@@ -141,7 +141,10 @@ class ReHoParcels(ReHoBase):
         )
         # Perform aggregation on reho map
         parcel_aggregation_input = {"data": reho_map}
-        output = parcel_aggregation.compute(input=parcel_aggregation_input)
+        output = parcel_aggregation.compute(
+            input=parcel_aggregation_input,
+            extra_input=extra_input,
+        )
         # Only use the first row and expand row dimension
         output["data"] = output["data"][0][np.newaxis, :]
         return output

junifer/markers/reho/reho_spheres.py

@@ -149,7 +149,9 @@ class ReHoSpheres(ReHoBase):
         )
         # Perform aggregation on reho map
         sphere_aggregation_input = {"data": reho_map}
-        output = sphere_aggregation.compute(input=sphere_aggregation_input)
+        output = sphere_aggregation.compute(
+            input=sphere_aggregation_input, extra_input=extra_input
+        )
         # Only use the first row and expand row dimension
         output["data"] = output["data"][0][np.newaxis, :]
         return output