Merge branch 'dev-v2.0.0' into simpleLflip

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
@@ -278,6 +284,7 @@ parse_args:
       - synthseg_v0.2
       - neonateT1w_v2
 
+
   --enable-bids-validation:
     help: |
       Enable validation of BIDS dataset. BIDS validation would be performed
@@ -294,7 +301,6 @@ parse_args:
     version: "1.5.2-pre.2"
 
 
-
 # --- surface specific configuration -- 
 
 autotop_labels:
@@ -308,6 +314,8 @@ surf_types:
     - outer
   dentate:
     - midthickness
+#    - inner
+#    - outer
 
 gifti_metric_types:
   hipp:
@@ -327,7 +335,14 @@ cifti_metric_types:
     - gyrification.dscalar
     - curvature.dscalar
 
-
+# params for detecting and removing outlier vertices
+outlier_opts:
+  outlierSmoothDist: 
+    unfoldiso: 15
+    0p5mm: 7
+    1mm: 3
+    2mm: 1
+  vertexOutlierThreshold: 3
 
 
 
@@ -364,6 +379,7 @@ template_available_hemis:
     - R
     - L
 
+
 template_files:
   CITI168:
     T1w: T1w_head_700um.nii.gz
@@ -418,13 +434,15 @@ template_files:
     dseg: tpl-ABAv3_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz
     coords: tpl-ABAv3_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
   bigbrain:
-    T1w: tpl-bigbrain_100um_T1w.nii.gz
+    T1w: tpl-bigbrain_1mm_merker.nii.gz
+    T2w: tpl-bigbrain_1mm_merker.nii.gz
     xfm_corobl: tpl-bigbrain_from-native_to-corobl_type-itk_affine.txt
-    crop_ref: tpl-bigbrain_hemi-{hemi}_space-corobl_desc-tissuemanual_40um_dseg.nii.gz
-    Mask_crop: tpl-bigbrain_hemi-{hemi}_space-corobl_desc-tissuemanual_40um_dseg.nii.gz
-    dseg: tpl-bigbrain_hemi-{hemi}_space-corobl_desc-tissuemanual_40um_dseg.nii.gz
+    crop_ref: tpl-bigbrain_hemi-{hemi}_space-corobl_100um_merker.nii.gz
+    Mask_crop: tpl-bigbrain_hemi-{hemi}_space-corobl_desc-tissuemanual_100um_dseg.nii.gz
+    dseg: tpl-bigbrain_hemi-{hemi}_space-corobl_desc-tissuemanual_100um_dseg.nii.gz
     coords: tpl-bigbrain_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
 
+
 atlas_files:
   multihist7:
     label_nii: sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz
@@ -582,6 +600,11 @@ unfold_vol_ref:
       - '2.5'
     orient: RPI
 
+unfold_crop_epsilon_fractions:
+    - 0
+    - 0
+    - 1 #in unfolded space voxels
+
 
 # space for uniform unfolded grid:
 #  currently only used for interpolating hipp subfields on surface
@@ -638,7 +661,8 @@ laplace_labels:
       - 7
     sink:
       - 0 
-
+    gm_noDG:
+      - 1
 
 output_spaces:
   - native
@@ -666,3 +690,4 @@ 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"],
@@ -147,6 +148,11 @@ include: "rules/qc.smk"
 include: "rules/myelin_map.smk"
 
 
+if config["native_surf"]:
+
+    include: "rules/native_surf.smk"
+
+
 if config["use_template_seg"]:
     if (
         "dseg" in config["template_files"][config["template"]]

hippunfold/workflow/rules/common.smk

@@ -40,55 +40,17 @@ def get_modality_suffix(modality):
 
 
 def get_final_spec():
-    if len(config["hemi"]) == 2:
-        specs = inputs[config["modality"]].expand(
-            bids(
-                root=root,
-                datatype="surf",
-                den="{density}",
-                space="{space}",
-                label="{autotop}",
-                suffix="surfaces.spec",
-                **inputs.subj_wildcards,
-            ),
-            density=config["output_density"],
-            space=ref_spaces,
-            autotop=config["autotop_labels"],
-            allow_missing=True,
-        )
-    else:
-        specs = inputs[config["modality"]].expand(
-            bids(
-                root=root,
-                datatype="surf",
-                den="{density}",
-                space="{space}",
-                hemi="{hemi}",
-                label="{autotop}",
-                suffix="surfaces.spec",
-                **inputs.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(
+    specs = []
+    specs.extend(
         inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="surf",
                 den="{density}",
-                suffix="{surfname}.surf.gii",
                 space="{space}",
                 hemi="{hemi}",
                 label="{autotop}",
+                suffix="surfaces.spec",
                 **inputs.subj_wildcards,
             ),
             density=config["output_density"],
@@ -99,16 +61,16 @@ def get_final_surf():
             allow_missing=True,
         )
     )
-    gii.extend(
+    specs.extend(
         inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="surf",
                 den="{density}",
-                suffix="{surfname}.surf.gii",
                 space="{space}",
                 hemi="{hemi}",
                 label="{autotop}",
+                suffix="surfaces.spec",
                 **inputs.subj_wildcards,
             ),
             density=config["output_density"],
@@ -119,7 +81,7 @@ def get_final_surf():
             allow_missing=True,
         )
     )
-    return gii
+    return specs
 
 
 def get_final_subfields():
@@ -373,7 +335,6 @@ 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 +198,26 @@ 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",
             **inputs.subj_wildcards
         ),
+    params:
+        dist=lambda wildcards: config["outlier_opts"]["outlierSmoothDist"][
+            wildcards.density
+        ],
+        threshold=config["outlier_opts"]["vertexOutlierThreshold"],
     output:
         gii=bids(
             root=work,
@@ -230,7 +235,7 @@ rule correct_nan_vertices1:
     container:
         config["singularity"]["autotop"]
     script:
-        "../scripts/fillnanvertices.py"
+        "../scripts/fillbadvertices.py"
 
 
 # morphological features, calculated in native space:
@@ -730,7 +735,7 @@ rule warp_gii_unfold2corobl2:
             datatype="surf",
             den="{density}",
             suffix="{surfname}.surf.gii",
-            desc="nonancorrect",
+            desc="nobadcorrect",
             space="corobl",
             hemi="{hemi}",
             label="{autotop}",
@@ -746,20 +751,25 @@ 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}",
             **inputs.subj_wildcards
         ),
+    params:
+        dist=lambda wildcards: config["outlier_opts"]["outlierSmoothDist"][
+            wildcards.density
+        ],
+        threshold=config["outlier_opts"]["vertexOutlierThreshold"],
     output:
         gii=bids(
             root=work,
@@ -776,7 +786,7 @@ rule correct_nan_vertices2:
     container:
         config["singularity"]["autotop"]
     script:
-        "../scripts/fillnanvertices.py"
+        "../scripts/fillbadvertices.py"
 
 
 # needed for if native_modality is corobl