docs/changes/newsfragments/274.bugfix

@@ -0,0 +1 @@
+Store native warped parcellations, coordinates and masks in element-scoped tempdirs for the pipeline to work by `Synchon Mandal`_

junifer/data/coordinates.py

@@ -240,24 +240,31 @@ def get_coordinates(
                 f"{target_data['space']} space for further computation."
             )
 
-        # Create tempdir
+        # Create component-scoped tempdir
         tempdir = WorkDirManager().get_tempdir(prefix="coordinates")
 
-        # Save existing coordinates
+        # Save existing coordinates to a component-scoped tempfile
         pretransform_coordinates_path = (
             tempdir / "pretransform_coordinates.txt"
         )
         np.savetxt(pretransform_coordinates_path, seeds)
 
-        # Create a tempfile for transformed coordinates output
-        std2imgcoord_out_path = tempdir / "coordinates_transformed.txt"
+        # Create element-scoped tempdir so that transformed coordinates is
+        # available later as numpy stores file path reference for
+        # loading on computation
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="coordinates"
+        )
+
+        # Create an element-scoped tempfile for transformed coordinates output
+        std2imgcoord_out_path = element_tempdir / "coordinates_transformed.txt"
         # Set std2imgcoord command
         std2imgcoord_cmd = [
             "std2imgcoord",
             f"-img {target_data['reference_path'].resolve()}",
             f"-warp {extra_input['Warp']['path'].resolve()}",
-            f"{pretransform_coordinates_path}",
-            f"> {std2imgcoord_out_path}",
+            f"{pretransform_coordinates_path.resolve()}",
+            f"> {std2imgcoord_out_path.resolve()}",
         ]
         # Call std2imgcoord
         std2imgcoord_cmd_str = " ".join(std2imgcoord_cmd)
@@ -272,8 +279,6 @@ def get_coordinates(
             shell=True,  # needed for respecting $PATH
             check=False,
         )
-        # Delete saved coordinates file
-        pretransform_coordinates_path.unlink()
         # Check for success or failure
         if std2imgcoord_process.returncode == 0:
             logger.info(

junifer/data/masks.py

@@ -344,15 +344,20 @@ def get_mask(  # noqa: C901
                 f"{target_data['space']} space for further computation."
             )
 
-        # Create tempdir
+        # Create component-scoped tempdir
         tempdir = WorkDirManager().get_tempdir(prefix="masks")
 
-        # Save mask image
+        # Save mask image to a component-scoped tempfile
         prewarp_mask_path = tempdir / "prewarp_mask.nii.gz"
         nib.save(mask_img, prewarp_mask_path)
 
-        # Create a tempfile for warped output
-        applywarp_out_path = tempdir / "mask_warped.nii.gz"
+        # Create element-scoped tempdir so that warped mask is
+        # available later as nibabel stores file path reference for
+        # loading on computation
+        element_tempdir = WorkDirManager().get_element_tempdir(prefix="masks")
+
+        # Create an element-scoped tempfile for warped output
+        applywarp_out_path = element_tempdir / "mask_warped.nii.gz"
         # Set applywarp command
         applywarp_cmd = [
             "applywarp",

junifer/data/parcellations.py

@@ -289,15 +289,22 @@ def get_parcellation(
                 f"{target_data['space']} space for further computation."
             )
 
-        # Create tempdir
+        # Create component-scoped tempdir
         tempdir = WorkDirManager().get_tempdir(prefix="parcellations")
 
-        # Save parcellation image
+        # Save parcellation image to a component-scoped tempfile
         prewarp_parcellation_path = tempdir / "prewarp_parcellation.nii.gz"
         nib.save(resampled_parcellation_img, prewarp_parcellation_path)
 
-        # Create a tempfile for warped output
-        applywarp_out_path = tempdir / "parcellation_warped.nii.gz"
+        # Create element-scoped tempdir so that warped parcellation is
+        # available later as nibabel stores file path reference for
+        # loading on computation
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="parcellations"
+        )
+
+        # Create an element-scoped tempfile for warped output
+        applywarp_out_path = element_tempdir / "parcellation_warped.nii.gz"
         # Set applywarp command
         applywarp_cmd = [
             "applywarp",

junifer/preprocess/fsl/bold_warper.py

@@ -35,7 +35,7 @@ class BOLDWarper(BasePreprocessor):
     ] = [
         {
             "name": "fsl",
-            "optional": True,
+            "optional": False,
             "commands": ["applywarp"],
         },
     ]