Enh/compute_subject_gm_mask

junifer/data/coordinates/_fsl_coordinates_warper.py

@@ -69,7 +69,7 @@ def warp(
             f"{pretransform_coordinates_path.resolve()}",
             "| img2imgcoord -mm",
             f"-src {target_data['path'].resolve()}",
-            f"-dest {target_data['reference_path'].resolve()}",
+            f"-dest {target_data['reference']["path"].resolve()}",
             f"-warp {warp_data['path'].resolve()}",
             f"> {transformed_coords_path.resolve()};",
             f"sed -i 1d {transformed_coords_path.resolve()}",

junifer/data/masks/_ants_mask_warper.py

@@ -46,18 +46,19 @@
             The mask image to transform.
         src : str
             The data type or template space to warp from.
-            It should be empty string if ``dst="T1w"``.
+            It should be empty string if ``dst="native"``.
         dst : str
             The data type or template space to warp to.
-            `"T1w"` is the only allowed data type and it uses the resampled T1w
-            found in ``target_data.reference_path``. The ``"reference_path"``
-            key is added when :class:`.SpaceWarper` is used.
+            `"native"` is the only allowed data type and it uses the resampled
+            T1w found in ``target_data.reference``. The 
+            ``"reference"`` key is added when :class:`.SpaceWarper` is
+            used or if the data is provided native space.
         target_data : dict
             The corresponding item of the data object to which the mask
             will be applied.
         warp_data : dict or None
             The warp data item of the data object. The value is unused if
-            ``dst!="T1w"``.
+            ``dst!="native"``.
 
         Returns
         -------
@@ -87,6 +88,10 @@
             # Warp data check
             if warp_data is None:
                 raise_error("No `warp_data` provided")
+            if "reference" not in target_data:
+                raise_error("No `reference` provided")
+            if "path" not in target_data["reference"]:
+                raise_error("No `path` provided in `reference`")
 
             logger.debug("Using ANTs for mask transformation")
 
@@ -104,7 +109,7 @@
                 "-n 'GenericLabel[NearestNeighbor]'",
                 f"-i {prewarp_mask_path.resolve()}",
                 # use resampled reference
-                f"-r {target_data['reference_path'].resolve()}",
+                f"-r {target_data['reference']["path"].resolve()}",
                 f"-t {warp_data['path'].resolve()}",
                 f"-o {warped_mask_path.resolve()}",
             ]

junifer/data/masks/_fsl_mask_warper.py

@@ -74,7 +74,7 @@ def warp(
             "--interp=nn",
             f"-i {prewarp_mask_path.resolve()}",
             # use resampled reference
-            f"-r {target_data['reference_path'].resolve()}",
+            f"-r {target_data['reference']["path"].resolve()}",
             f"-w {warp_data['path'].resolve()}",
             f"-o {warped_mask_path.resolve()}",
         ]