🚧 WIP ♻️ Differentiate longitudinal template images from session images in longitudinal template space

Author: shnizzedy

CPAC/longitudinal/wf/anat.py

@@ -90,8 +90,8 @@ def pick_map(
     name="mask_longitudinal_T1w_brain",
     config=["longitudinal_template_generation"],
     switch=["run"],
-    inputs=["space-longitudinal_desc-brain_T1w"],
-    outputs=["space-longitudinal_desc-brain_mask"],
+    inputs=["longitudinal-template_space-longitudinal_desc-brain_T1w"],
+    outputs=["longitudinal-template_space-longitudinal_desc-brain_mask"],
 )
 def mask_longitudinal_T1w_brain(
     wf, cfg, strat_pool, pipe_num, opt=None
@@ -103,10 +103,17 @@ def mask_longitudinal_T1w_brain(
     )
     brain_mask.inputs.args = "-bin"
 
-    node, out = strat_pool.get_data("space-longitudinal_desc-brain_T1w")
+    node, out = strat_pool.get_data(
+        "longitudinal-template_space-longitudinal_desc-brain_T1w"
+    )
     wf.connect(node, out, brain_mask, "in_file")
 
-    outputs = {"space-longitudinal_desc-brain_mask": (brain_mask, "out_file")}
+    outputs = {
+        "longitudinal-template_space-longitudinal_desc-brain_mask": (
+            brain_mask,
+            "out_file",
+        )
+    }
 
     return (wf, outputs)
 
@@ -115,11 +122,9 @@ def mask_longitudinal_T1w_brain(
     name="warp_longitudinal_T1w_to_template",
     config=["longitudinal_template_generation"],
     switch=["run"],
-    option_key="using",
-    option_val="C-PAC legacy",
     inputs=[
         (
-            "space-longitudinal_desc-brain_T1w",
+            "longitudinal-template_space-longitudinal_desc-brain_T1w",
             "from-longitudinal_to-template_mode-image_xfm",
         ),
         "T1w-brain-template",
@@ -155,7 +160,9 @@ def warp_longitudinal_T1w_to_template(
             "anatomical_registration"
         ]["registration"]["FSL-FNIRT"]["interpolation"]
 
-    node, out = strat_pool.get_data("space-longitudinal_desc-brain_T1w")
+    node, out = strat_pool.get_data(
+        "longitudinal-template_space-longitudinal_desc-brain_T1w"
+    )
     wf.connect(node, out, apply_xfm, "inputspec.input_image")
 
     node, out = strat_pool.get_data("T1w-brain-template")
@@ -164,7 +171,12 @@ def warp_longitudinal_T1w_to_template(
     node, out = strat_pool.get_data("from-longitudinal_to-template_mode-image_xfm")
     wf.connect(node, out, apply_xfm, "inputspec.transform")
 
-    outputs = {"space-template_desc-brain_T1w": (apply_xfm, "outputspec.output_image")}
+    outputs = {
+        "longitudinal-template_space-template_desc-brain_T1w": (
+            apply_xfm,
+            "outputspec.output_image",
+        )
+    }
 
     return (wf, outputs)
 
@@ -175,7 +187,7 @@ def warp_longitudinal_T1w_to_template(
     switch=["run"],
     inputs=[
         (
-            "space-longitudinal_desc-brain_T1w",
+            "longitudinal-template_space-longitudinal_desc-brain_T1w",
             [
                 "from-longitudinal_to-T1w_mode-image_desc-linear_xfm",
                 "from-T1w_to-longitudinal_mode-image_desc-linear_xfm",
@@ -213,7 +225,7 @@ def warp_longitudinal_seg_to_T1w(
     pipe_num: int,
     opt: Optional[str] = None,
 ) -> NODEBLOCK_RETURN:
-    """Transform anatomical images from longitudinal space template space."""
+    """Transform anatomical segmentation from longitudinal template to T1w space."""
     outputs = {}
     if strat_pool.check_rpool("from-longitudinal_to-T1w_mode-image_desc-linear_xfm"):
         xfm_prov = strat_pool.get_cpac_provenance(
@@ -229,7 +241,7 @@ def warp_longitudinal_seg_to_T1w(
         )
         reg_tool = check_prov_for_regtool(xfm_prov)
         # create inverse xfm if we don't have it
-        invt = pe.Node(interface=fsl.ConvertXFM(), name="convert_xfm")
+        invt = pe.Node(interface=fsl.ConvertXFM(), name=f"convert_xfm_{pipe_num}")
         invt.inputs.invert_xfm = True
         wf.connect(
             *strat_pool.get_data("from-T1w_to-longitudinal_mode-image_desc-linear_xfm"),
@@ -246,7 +258,9 @@ def warp_longitudinal_seg_to_T1w(
     )
     wf.connect(*xfm, warp, "postmat")
     wf.connect(
-        *strat_pool.get_data("space-longitudinal_desc-brain_T1w"), warp, "reference"
+        *strat_pool.get_data("longitudinal-template_space-longitudinal_desc-brain_T1w"),
+        warp,
+        "reference",
     )
     outputs["from-longitudinal_to-T1w_mode-image_desc-linear_warp"] = warp, "out_file"
 
@@ -281,7 +295,9 @@ def warp_longitudinal_seg_to_T1w(
                 "anatomical_registration"
             ]["registration"]["FSL-FNIRT"]["interpolation"]
 
-        node, out = strat_pool.get_data("space-longitudinal_desc-brain_T1w")
+        node, out = strat_pool.get_data(
+            "longitudinal-template_space-longitudinal_desc-brain_T1w"
+        )
         wf.connect(node, out, apply_xfm, "inputspec.input_image")
 
         node, out = strat_pool.get_data("T1w-brain-template")
@@ -369,7 +385,7 @@ def anat_longitudinal_wf(
         name="template_node_brain",
     )
 
-    config.pipeline_setup["pipeline_name"] = f"longitudinal_{orig_pipe_name}"
+    config.pipeline_setup["pipeline_name"] = f"longitudinal-template_{orig_pipe_name}"
 
     num_sessions = len(strats_dct["desc-brain_T1w"])
     merge_brains = pe.Node(Merge(num_sessions), name="merge_brains")
@@ -381,9 +397,9 @@ def anat_longitudinal_wf(
         )
         wf._connect_node_or_path_for_merge(merge_skulls, strats_dct, "desc-head_T1w", i)
 
-    long_id = f"longitudinal_{subject_id}_strat-desc-brain_T1w"
+    long_id = f"longitudinal-template_{subject_id}_desc-brain_T1w"
 
-    wf, rpool = initiate_rpool(wf, config, part_id=long_id)
+    wf, rpool = initiate_rpool(wf, config, part_id=subject_id)
 
     match config["longitudinal_template_generation", "using"]:
         case "C-PAC legacy":
@@ -449,7 +465,7 @@ def anat_longitudinal_wf(
 
     for suffix in ["", "-template"]:
         rpool.set_data(
-            f"space-longitudinal_desc-brain_T1w{suffix}",
+            f"longitudinal-template_space-longitudinal_desc-brain_T1w{suffix}",
             brain_template_node,
             brain_output,
             {},
@@ -459,7 +475,7 @@ def anat_longitudinal_wf(
 
         for desc in ["head", "reorient"]:
             rpool.set_data(
-                f"space-longitudinal_desc-{desc}_T1w{suffix}",
+                f"longitudinal-template_space-longitudinal_desc-{desc}_T1w{suffix}",
                 wholehead_template_node,
                 head_output,
                 {},
@@ -477,9 +493,9 @@ def anat_longitudinal_wf(
         wf,
         config,
         add_excl=[
-            "space-longitudinal_desc-brain_T1w",
-            "space-longitudinal_desc-reorient_T1w",
-            "space-longitudinal_desc-brain_mask",
+            "longitudinal-template_space-longitudinal_desc-brain_T1w",
+            "longitudinal-template_space-longitudinal_desc-reorient_T1w",
+            "longitudinal-template_space-longitudinal_desc-brain_mask",
         ],
     )
     wf = connect_pipeline(wf, config, rpool, pipeline_blocks)
@@ -580,14 +596,6 @@ def anat_longitudinal_wf(
                     "",
                     head_select_sess.name,
                 )
-                rpool.set_data(
-                    "from-T1w_to-longitudinal_mode-image_desc-linear_xfm",
-                    head_select_sess,
-                    "warp_path",
-                    {},
-                    "",
-                    head_select_sess.name,
-                )
 
         rpool.set_data(
             "space-longitudinal_desc-brain_T1w",

CPAC/pipeline/engine.py

@@ -152,6 +152,9 @@ def _set_id_parts(self) -> None:
         """Set part_id and ses_id."""
         unique_id = self.name
         setattr(self, "_part_id", unique_id.split("_")[0])
+        if "_" not in unique_id:
+            setattr(self, "_ses_id", None)
+            return
         ses_id = unique_id.split("_")[1]
         if "ses-" not in ses_id:
             ses_id = f"ses-{ses_id}"
@@ -1156,9 +1159,15 @@ def gather_pipes(self, wf, cfg, all=False, add_incl=None, add_excl=None):
             for pipe_idx in self.rpool[resource]:
                 out_dir = cfg.pipeline_setup["output_directory"]["path"]
                 pipe_name = cfg.pipeline_setup["pipeline_name"]
-                container = os.path.join(
-                    f"pipeline_{pipe_name}", self.part_id, self.ses_id
-                )
+                if resource.startswith("longitudinal-template_"):
+                    container = os.path.join(f"pipeline_{pipe_name}", self.part_id)
+                else:
+                    container = os.path.join(
+                        f"pipeline_{pipe_name}", self.part_id, self.ses_id
+                    )
+                resource_name = self.get_name()
+                if resource_name.startswith("longitudinal-template_"):
+                    resource_name = resource_name[22:]
                 filename = f"{self.get_name()}_{res_in_filename(self.cfg, resource)}"
 
                 out_path = os.path.join(out_dir, container, subdir, filename)