- put things into surf instead of surf_

- cleanup filenames, remove desc from output
- add cli option, revert some tweaks
- extrapolation of coords before isosurf is causing issues.. remove holes
some other way instead...
- linting

hippunfold/config/snakebids.yml

@@ -195,6 +195,12 @@ parse_args:
     default: False
     action: store_true
 
+  --native_surf:
+    help: 'Use native surf workflow to generate isosurfaces in native space, and use wb_command tools to resample. Note: this currently disables unfolded registration if applied (until it is implemented).'
+    default: False
+    action: store_true
+
+
   --generate_myelin_map:
     help: 'Generate myelin map using T1w divided by T2w, and map to surface with ribbon approach. Requires both T1w and T2w images to be present. (default: %(default)s)'
     default: False
@@ -693,3 +699,4 @@ no_unfolded_reg: False
 root: results
 use_template_seg: False
 template_seg_smoothing_factor: 2
+native_surf: False

hippunfold/workflow/Snakefile

@@ -62,9 +62,10 @@ 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"]:
+if not config["atlas"] == ["multihist7"] or config["native_surf"]:
     config["no_unfolded_reg"] = True
 
+
 inputs = snakebids.generate_inputs(
     bids_dir=config["bids_dir"],
     pybids_inputs=config["pybids_inputs"],
@@ -127,13 +128,29 @@ if config["modality"] == "hippb500":
 
 
 include: "rules/autotop.smk"
+
+
 include: "rules/warps.smk"
+
+
 include: "rules/gifti.smk"
+
+
 include: "rules/subfields.smk"
+
+
 include: "rules/resample_final_to_crop_native.smk"
+
+
 include: "rules/qc.smk"
+
+
 include: "rules/myelin_map.smk"
-include: "rules/native_surf.smk"
+
+
+if config["native_surf"]:
+
+    include: "rules/native_surf.smk"
 
 
 if config["use_template_seg"]: