Still WIP

TODO:
  - make alternative script for volumetric subfield labelling that
uses label_gifti intstead of label_nifti
  - the volumetric targets are all turned off for now until that is
done, since the cropref space relies on the subfields
  - add some smoothing for native surfaces (maybe another PR)
  - verify that the unfoldreg warping is being performed properly
(compare with images, or make a toy example)
     - try with a single subject atlas, where the atlas is defined on
it's own unfolded tesselation instead of unfoldiso - could make some
target rules to generate the files for this (e.g. the subject metrics
in unfold 2d slice, along with native and unfold meshes)

hippunfold/workflow/Snakefile

@@ -62,7 +62,7 @@ if config["skip_inject_template_labels"]:  # TODO do we need this?
 limit_to_list.add(config["modality"])
 
 # if atlas doesn't contain alignment features
-if not config["atlas"] == ["multihist7"] or config["native_surf"]:
+if not config["atlas"] == ["multihist7"]: 
     config["no_unfolded_reg"] = True
 
 
@@ -172,7 +172,6 @@ else:
 
     include: "rules/shape_inject.smk"
 
-
 rule all:
     input:
         get_final_output(),

hippunfold/workflow/rules/common.smk

@@ -335,11 +335,11 @@ def get_final_qc():
 def get_final_subj_output():
     subj_output = []
     subj_output.extend(get_final_spec())
-    subj_output.extend(get_final_subfields())
-    subj_output.extend(get_final_coords())
-    subj_output.extend(get_final_transforms())
-    subj_output.extend(get_final_anat())
-    subj_output.extend(get_final_qc())
+   # subj_output.extend(get_final_subfields())
+  #  subj_output.extend(get_final_coords())
+   # subj_output.extend(get_final_transforms())
+   # subj_output.extend(get_final_anat())
+   # subj_output.extend(get_final_qc())
     return subj_output
 
 
@@ -349,25 +349,7 @@ def get_final_output():
     else:
         subj_output = get_final_work_tar()
 
-    final_output = []
-
-    modality_suffix = get_modality_suffix(config["modality"])
-    modality_key = config["modality"]
-
-    # use a zip list for subject/session:
-    zip_list = inputs[modality_key].zip_lists
-    if "session" in zip_list:
-        zip_list = snakebids.filter_list(
-            zip_list,
-            {"session": inputs[config["modality"]].zip_lists["session"]},
-        )
-    final_output.extend(
-        expand(
-            expand(subj_output, zip, allow_missing=True, **zip_list),
-            modality_suffix=modality_suffix,
-        )
-    )
-    return final_output
+    return subj_output
 
 
 if "corobl" in ref_spaces:

hippunfold/workflow/rules/native_surf.smk

@@ -16,14 +16,14 @@ resample_from_density = (
 )
 
 
-unfoldreg_metrics = [ 'thickness', 'curvature', 'gyrification']
+# could allow user to select additional metrics (e.g. from bold, dwi ...)
+unfoldreg_metrics = [ 'thickness', 'curvature', 'gyrification']  
 
 
 # if we aren't doing unfolded reg, then we have these rules override correct_bad_vertices2
 ruleorder: resample_native_surf >  cp_template_to_unfold
-#ruleorder: cp_template_to_unfold > resample_native_surf
-ruleorder: resample_native_surf > correct_bad_vertices2 
-ruleorder: warp_midthickness_to_inout > correct_bad_vertices2
+#ruleorder: resample_native_surf > correct_bad_vertices2 
+#ruleorder: warp_midthickness_to_inout > correct_bad_vertices2
 ruleorder: unfold_spring_model > warp_unfold_native_to_unfoldreg
 
 rule prep_hipp_coords_for_meshing:
@@ -497,6 +497,46 @@ rule warp_midthickness_to_inout:
         " -surface-secondary-type {params.secondary_type}"
 
 
+# warp native surface from corobl to T1w/T2w
+rule affine_gii_corobl_to_modality:
+    input:
+        gii=bids(
+            root=work,
+            datatype="surf",
+            suffix="{surfname}.surf.gii",
+            space="corobl",
+            hemi="{hemi}",
+            label="{autotop}",
+            **inputs.subj_wildcards
+        ),
+        xfm=bids(
+            root=work,
+            datatype="warps",
+            **inputs.subj_wildcards,
+            suffix="xfm.txt",
+            from_="{native_modality}",
+            to="corobl",
+            desc="affine",
+            type_="ras"
+        ),
+    output:
+        gii=bids(
+            root=root,
+            datatype="surf",
+            suffix="{surfname}.surf.gii",
+            space="{native_modality}",
+            hemi="{hemi}",
+            label="{autotop,hipp|dentate}",
+            **inputs.subj_wildcards
+        ),
+    container:
+        config["singularity"]["autotop"]
+    group:
+        "subj"
+    shell:
+        "wb_command -surface-apply-affine {input.gii} {input.xfm} {output.gii}"
+
+
 
 rule unfold_spring_model:
     input:
@@ -801,20 +841,7 @@ rule native_metric_to_unfold_nii:
         " -ribbon-constrained {input.inner_surf} {input.outer_surf}"
 
 
-print(bids(
-            root=work,
-            suffix="xfm.nii.gz",
-            datatype="warps",
-            desc="SyN",
-            from_="native",
-            to_="{atlas}",
-            space="unfold",
-            type_="itk",
-            hemi="{hemi}",
-            label="{label}",
-            **inputs.subj_wildcards,
-        ))
-
+
 rule unfoldreg:
     """performs 2D registration in unfolded space as in [reference paper]
     this is done in a shadow directory to get rid of the tmp files generated by ants."""
@@ -1000,7 +1027,7 @@ rule warp_unfold_native_to_unfoldreg:
             datatype="warps",
             desc="SyN",
             from_="native",
-            to="{atlas}",
+            to=config['atlas'][0],
             space="unfold",
             type_="surface",
             hemi="{hemi}",
@@ -1017,7 +1044,6 @@ rule warp_unfold_native_to_unfoldreg:
             datatype="surf",
             suffix="{surfname}.surf.gii",
             space="unfoldreg",
-            atlas="{atlas}",
             hemi="{hemi}",
             label="{label}",
             **inputs.subj_wildcards
@@ -1088,7 +1114,7 @@ rule resample_subfields_to_native_surf:
 
 rule resample_native_surf:
     input:
-        native_corobl=bids(
+        native=bids(
             root=work,
             datatype="surf",
             suffix="{surf_name}.surf.gii",
@@ -1109,21 +1135,19 @@ rule resample_native_surf:
             datatype="surf",
             suffix="midthickness.surf.gii",
             space="unfoldreg",
-            atlas="{atlas}",
             hemi="{hemi}",
             label="{label}",
             **inputs.subj_wildcards
         ),
 
     output:
-        native_corobl_resampled=bids(
+        native_resampled=bids(
             root=work,
             datatype="surf",
             suffix="{surf_name,midthickness}.surf.gii",
             space="{space}",
             den="{density}",
             hemi="{hemi}",
-            atlas="{atlas}",
             label="{label}",
             **inputs.subj_wildcards,
         ),
@@ -1133,7 +1157,7 @@ rule resample_native_surf:
     group:
         "subj"
     shell:
-        "wb_command -surface-resample {input.native_corobl} {input.native_unfold} {input.ref_unfold} BARYCENTRIC {output.native_corobl_resampled} -bypass-sphere-check"
+        "wb_command -surface-resample {input.native} {input.native_unfold} {input.ref_unfold} BARYCENTRIC {output.native_resampled} -bypass-sphere-check"
 
 
 rule resample_native_metric:
@@ -1142,7 +1166,7 @@ rule resample_native_metric:
             root=work,
             datatype="surf",
             suffix="{metric}.{metrictype}.gii",
-            space="{space}",
+            space="corobl", #metrics always calculated in corobl
             hemi="{hemi}",
             label="{label}",
             **inputs.subj_wildcards
@@ -1159,20 +1183,18 @@ rule resample_native_metric:
             datatype="surf",
             suffix="midthickness.surf.gii",
             space="unfoldreg",
-            atlas="{atlas}",
             hemi="{hemi}",
             label="{label}",
             **inputs.subj_wildcards
         ),
 
     output:
         metric_resampled=bids(
-            root=work,
+            root=root,
             datatype="surf",
             suffix="{metric}.{metrictype,shape|func}.gii",
             space="{space}",
             den="{density}",
-            atlas="{atlas}",
             hemi="{hemi}",
             label="{label}",
             **inputs.subj_wildcards,
@@ -1185,5 +1207,56 @@ rule resample_native_metric:
     shell:
         "wb_command -metric-resample {input.native_metric} {input.native_unfold} {input.ref_unfold} BARYCENTRIC {output.metric_resampled} -bypass-sphere-check"
 
+rule cp_surf_to_root:
+    input:
+        native_resampled=bids(
+            root=work,
+            datatype="surf",
+            suffix="{surf_name,midthickness}.surf.gii",
+            space="{space}",
+            den="{density}",
+            hemi="{hemi}",
+            label="{label}",
+            **inputs.subj_wildcards,
+        ),
+    output:
+        native_resampled=bids(
+            root=root,
+            datatype="surf",
+            suffix="{surf_name,midthickness}.surf.gii",
+            space="{space}",
+            den="{density}",
+            hemi="{hemi}",
+            label="{label}",
+            **inputs.subj_wildcards,
+        ),
+    shell:
+        "cp {input} {output}"
+"""
+rule cp_metric_to_root:
+    input: 
+         metric_resampled=bids(
+            root=work,
+            datatype="surf",
+            suffix="{metricname}.{metrictype}.gii",
+            space="{space}",
+            den="{density}",
+            atlas=config['atlas'][0],
+            hemi="{hemi}",
+            label="{label}",
+            **inputs.subj_wildcards,
+        ),
+    output:
+         metric_resampled=bids(
+            root=root,
+            datatype="surf",
+            suffix="{metricname}.{metrictype,shape|func}.gii",
+            space="{space}",
+            den="{density}",
+            hemi="{hemi}",
+            label="{label}",
+            **inputs.subj_wildcards,
+        ),
+    shell: 'cp {input} {output}'
 
-
+"""

hippunfold/workflow/rules/subfields.smk

@@ -73,6 +73,8 @@ def skip_unfoldreg_option_subfields(wildcards):
     return label_nii
 
 
+#TODO: replace this with a function that operates on the label gifti instead for native_warp workflow
+# to avoid use of the unfold2native warps  
 rule label_subfields_from_vol_coords_corobl:
     """ Label subfields using the volumetric coords and atlas subfield labels"""
     input: