Naturalinterpolation

hippunfold/config/snakebids.yml

@@ -327,18 +327,23 @@ parse_args:
       - synthseg_v0.2
       - neonateT1w_v2
 
+
+
+# --- surface specific configuration -- 
+
 autotop_labels:
   - 'hipp'
   - 'dentate'
 
-
 surf_types:
   hipp:
     - midthickness
     - inner
     - outer
   dentate:
     - midthickness
+#    - inner
+#    - outer
 
 gifti_metric_types:
   hipp:
@@ -358,7 +363,13 @@ cifti_metric_types:
     - gyrification.dscalar
     - curvature.dscalar
 
-
+# params for detecting and removing outlier vertices
+outlierSmoothDist: 
+  unfoldiso: 15
+  0p5mm: 7
+  1mm: 3
+  2mm: 1
+vertexOutlierThreshold: 3
 
 
 
@@ -601,7 +612,7 @@ unfold_vol_ref:
 unfold_crop_epsilon_fractions:
     - 0
     - 0
-    - 0.0625 #1/16
+    - 1
 
 # space for uniform unfolded grid:
 #  currently only used for interpolating hipp subfields on surface

hippunfold/workflow/rules/common.smk

@@ -24,41 +24,69 @@ def get_modality_suffix(modality):
 
 
 def get_final_spec():
-    if len(config["hemi"]) == 2:
-        specs = expand(
+    specs = expand(
+        bids(
+            root=root,
+            datatype="surf",
+            den="{density}",
+            space="{space}",
+            hemi="{hemi}",
+            label="{autotop}",
+            suffix="surfaces.spec",
+            **config["subj_wildcards"],
+        ),
+        density=config["output_density"],
+        space=ref_spaces,
+        hemi=config["hemi"],
+        autotop=config["autotop_labels"],
+        allow_missing=True,
+    )
+    return specs
+
+
+def get_final_surf():
+    gii = []
+    gii.extend(
+        expand(
             bids(
                 root=root,
                 datatype="surf",
                 den="{density}",
+                suffix="{surfname}.surf.gii",
                 space="{space}",
+                hemi="{hemi}",
                 label="{autotop}",
-                suffix="surfaces.spec",
                 **config["subj_wildcards"],
             ),
             density=config["output_density"],
             space=ref_spaces,
+            hemi=config["hemi"],
             autotop=config["autotop_labels"],
+            surfname=config["surf_types"]["hipp"],
             allow_missing=True,
         )
-    else:
-        specs = expand(
+    )
+    gii.extend(
+        expand(
             bids(
                 root=root,
                 datatype="surf",
                 den="{density}",
+                suffix="{surfname}.surf.gii",
                 space="{space}",
                 hemi="{hemi}",
                 label="{autotop}",
-                suffix="surfaces.spec",
                 **config["subj_wildcards"],
             ),
             density=config["output_density"],
             space=ref_spaces,
             hemi=config["hemi"],
             autotop=config["autotop_labels"],
+            surfname=config["surf_types"]["dentate"],
             allow_missing=True,
         )
-    return specs
+    )
+    return gii
 
 
 def get_final_subfields():
@@ -313,6 +341,7 @@ def get_final_qc():
 def get_final_subj_output():
     subj_output = []
     subj_output.extend(get_final_spec())
+    subj_output.extend(get_final_surf())
     subj_output.extend(get_final_subfields())
     subj_output.extend(get_final_coords())
     subj_output.extend(get_final_transforms())

hippunfold/workflow/rules/gifti.smk

@@ -181,7 +181,7 @@ rule warp_gii_unfold2corobl1:
             datatype="surf",
             den="{density}",
             suffix="{surfname}.surf.gii",
-            desc="nonancorrect",
+            desc="nobadcorrect",
             space="corobl",
             unfoldreg="none",
             hemi="{hemi}",
@@ -198,21 +198,24 @@ rule warp_gii_unfold2corobl1:
         " -surface-secondary-type {params.secondary_type}"
 
 
-# previous rule seems to be where nan vertices emerge, so we'll correct them here immediately after
-rule correct_nan_vertices1:
+# previous rule seems to be where bad vertices emerge, so we'll correct them here immediately after
+rule correct_bad_vertices1:
     input:
         gii=bids(
             root=work,
             datatype="surf",
             den="{density}",
             suffix="{surfname}.surf.gii",
-            desc="nonancorrect",
+            desc="nobadcorrect",
             space="corobl",
             unfoldreg="none",
             hemi="{hemi}",
             label="hipp",
             **config["subj_wildcards"]
         ),
+    params:
+        dist=lambda wildcards: config["outlierSmoothDist"][wildcards.density],
+        threshold=config["vertexOutlierThreshold"],
     output:
         gii=bids(
             root=work,
@@ -230,7 +233,7 @@ rule correct_nan_vertices1:
     container:
         config["singularity"]["autotop"]
     script:
-        "../scripts/fillnanvertices.py"
+        "../scripts/fillbadvertices.py"
 
 
 # morphological features, calculated in native space:
@@ -730,7 +733,7 @@ rule warp_gii_unfold2corobl2:
             datatype="surf",
             den="{density}",
             suffix="{surfname}.surf.gii",
-            desc="nonancorrect",
+            desc="nobadcorrect",
             space="corobl",
             hemi="{hemi}",
             label="{autotop}",
@@ -746,20 +749,23 @@ rule warp_gii_unfold2corobl2:
         " -surface-secondary-type {params.secondary_type}"
 
 
-# previous rule seems to be where nan vertices emerge, so we'll correct them here immediately after
-rule correct_nan_vertices2:
+# previous rule seems to be where bad vertices emerge, so we'll correct them here immediately after
+rule correct_bad_vertices2:
     input:
         gii=bids(
             root=work,
             datatype="surf",
             den="{density}",
             suffix="{surfname}.surf.gii",
-            desc="nonancorrect",
+            desc="nobadcorrect",
             space="corobl",
             hemi="{hemi}",
             label="{autotop}",
             **config["subj_wildcards"]
         ),
+    params:
+        dist=lambda wildcards: config["outlierSmoothDist"][wildcards.density],
+        threshold=config["vertexOutlierThreshold"],
     output:
         gii=bids(
             root=work,
@@ -776,7 +782,7 @@ rule correct_nan_vertices2:
     container:
         config["singularity"]["autotop"]
     script:
-        "../scripts/fillnanvertices.py"
+        "../scripts/fillbadvertices.py"
 
 
 # needed for if native_modality is corobl

hippunfold/workflow/rules/warps.smk

@@ -226,8 +226,6 @@ rule create_warps_hipp:
             hemi="{hemi}",
             suffix="create_warps-hipp.txt"
         ),
-    container:
-        config["singularity"]["autotop"]
     script:
         "../scripts/create_warps.py"
 
@@ -294,7 +292,6 @@ rule create_warps_dentate:
         ),
         labelmap=get_labels_for_laplace,
     params:
-        interp_method="linear",
         gm_labels=lambda wildcards: config["laplace_labels"]["PD"]["sink"],
         epsilon=lambda wildcards: config["unfold_crop_epsilon_fractions"],
     resources:
@@ -353,8 +350,6 @@ rule create_warps_dentate:
             hemi="{hemi}",
             suffix="create_warps-dentate.txt"
         ),
-    container:
-        config["singularity"]["autotop"]
     script:
         "../scripts/create_warps.py"