Multiple atlases updating docs & coding style

.github/workflows/python-testing.yml

@@ -174,6 +174,11 @@ jobs:
     - name: Test modality T1w with freesurfer atlas
       run: |
         poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas freesurfer
+    - name: Test modality T1w with bigbrain and freesurfer atlas
+      run: |
+        poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas bigbrain freesurfer
+
+
 
 
 

docs/tutorials/outputs.md

@@ -89,22 +89,53 @@ equivalently, the scaling or distortion factor when unfolding:
 
     sub-{subject}
      └── surf
-         └── sub-001_hemi-R_space-T1w_den-0p5mm_{thickness,curvature,gyrification}.shape.gii
+         └── sub-001_hemi-{L,R}_space-T1w_den-0p5mm_label-hipp_{thickness,curvature,gyrification}.shape.gii
+         └── sub-001_hemi-{L,R}_space-T1w_den-0p5mm_label-dentate_{curvature,gyrification}.shape.gii
 
 These metrics are shown in both folded and unfolded space in the images
 below. Note that these results are from group-averaged data and so
 individual subject maps may show considerably more variability.
 
 ![image](../images/metrics.png)
 
+
+### surface labels
+
+The subfield labels from unfolded atlases are also provided for each 
+subject, in `.label.gii` format. Analogous to the volume-based labels,
+the name of the atlas (default: `bigbrain`) is in the file name.
+
+    sub-{subject}
+     └── surf
+         └── sub-001_hemi-{L,R}_space-T1w_den-0p5mm_label-hipp_atlas-bigbrain_subfields.label.gii
+
+
+### cifti files
+
+In addition to lateralized `.shape.gii` and `.label.gii` metrics and labels,
+we also provide data mapped to hippocampi from hemispheres in a single
+file using the corresponding CIFTI formats, `.dscalar.nii` and `.dlabel.nii`. 
+Note: since CIFTI does not support hippocampus
+surfaces (yet), we make use of the `CORTEX_LEFT` and `CORTEX_RIGHT` labels for
+the hippocampal surfaces. 
+
+    sub-{subject}
+     └── surf
+         ├── sub-001_space-T1w_den-0p5mm_label-{hipp,dentate}_{thickness,curvature,gyrification}.dscalar.nii
+         └── sub-001_space-T1w_den-0p5mm_label-hipp_atlas-bigbrain_subfields.dlabel.nii
+
+
+### spec files
+
 Finally, these files are packaged together for easy viewing in
 Connectome Workbench, `wb_view`, in the following `.spec` files, for
-each hemisphere separately, and combined:
+each hemisphere and structure separately, and combined:
 
     sub-{subject}
      └── surf
-         ├── sub-001_hemi-R_space-T1w_den-0p5mm_surfaces.spec
-         └── sub-001_space-T1w_den-0p5mm_surfaces.spec
+         ├── sub-001_hemi-{L,R}_space-T1w_den-0p5mm_label-{hipp,dentate}_surfaces.spec
+         └── sub-001_space-T1w_den-0p5mm_label-{hipp,dentate}_surfaces.spec
+
 
 ### New: label-dentate
 
@@ -114,7 +145,7 @@ These are illustrated in the following image (orange represents the usual hippoc
 
 ![image](../images/dentate_cor.png)
 
-Note that the dentate uses the same unfolding methods as the rest of the hippocampus, but with several caveats. Given its small size, its boundaries are not easily deliminated and so `inner`, `outer`, and `thickness` gifti surfaces are omitted. Furthermore, Laplace coordinates and therefore vertex spacing are not guaranteed to be topoligically equivalent as they are obtained through volumetric registration with the template shape injection step of this workflow.  
+Note that the dentate uses the same unfolding methods as the rest of the hippocampus, but with several caveats. Given its small size, its boundaries are not easily deliminated and so `inner`, `outer`, and `thickness` gifti surfaces are omitted. Furthermore, Laplace coordinates and therefore vertex spacing are not guaranteed to be topologically equivalent as they are obtained through volumetric registration with the template shape injection step of this workflow.  
 
 Corresponding `coords` and `warp` files are also generated.
 

hippunfold/config/snakebids.yml

@@ -283,27 +283,26 @@ surf_types:
   dentate:
     - midthickness
 
-gifti_types:
+gifti_metric_types:
   hipp:
     - gyrification.shape 
     - curvature.shape
     - thickness.shape
-    - subfields.label
   dentate:
     - gyrification.shape 
     - curvature.shape
 
-cifti_types: 
+cifti_metric_types: 
   hipp:
     - gyrification.dscalar
     - curvature.dscalar
     - thickness.dscalar
-    - subfields.dlabel
   dentate:
     - gyrification.dscalar
     - curvature.dscalar
 
-
+
+
 
 
 #--- workflow specific configuration -- 

hippunfold/workflow/rules/gifti.smk

@@ -679,37 +679,101 @@ def get_cmd_spec_file(wildcards, input, output):
     return " && ".join(cmds)
 
 
-def concatenate_subfield_atlases(wildcards, types_list):
-    # only the subfields gii files have an atlas tag. This concatenates it on.
-    if type(types_list) == str:
-        types_list = list(types_list.split())
-    for ii in range(len(types_list)):
-        if "subfields" in types_list[ii]:
-            if "atlas" not in types_list[ii]:
-                orig = types_list[ii]
-                del types_list[ii]
-                for i in range(len(config["atlas"])):
-                    types_list.append("atlas-" + config["atlas"][i] + "_" + orig)
-    return types_list
-
-
-def get_cifti_types(wildcards):
-    types_list = config["cifti_types"][wildcards.label]
-    types_list = concatenate_subfield_atlases(wildcards, types_list)
+def get_cifti_metric_types(label):
+    types_list = config["cifti_metric_types"][label]
     if config["generate_myelin_map"]:
         types_list.append("myelin.dscalar")
     return types_list
 
 
-def get_gifti_types(wildcards):
-    types_list = config["gifti_types"][wildcards.label]
-    types_list = concatenate_subfield_atlases(wildcards, types_list)
+def get_gifti_metric_types(label):
+    types_list = config["gifti_metric_types"][label]
     if config["generate_myelin_map"]:
         types_list.append("myelin.shape")
     return types_list
 
 
-rule create_spec_file:
+rule create_spec_file_hipp:
+    input:
+        metrics=lambda wildcards: expand(
+            bids(
+                root=root,
+                datatype="surf",
+                den="{density}",
+                suffix="{metric}.gii",
+                space="{space}",
+                hemi="{hemi}",
+                label="{label}",
+                **config["subj_wildcards"]
+            ),
+            metric=get_gifti_metric_types(wildcards.label),
+            allow_missing=True,
+        ),
+        subfields=lambda wildcards: expand(
+            bids(
+                root=root,
+                datatype="surf",
+                den="{density}",
+                suffix="subfields.label.gii",
+                space="{space}",
+                hemi="{hemi}",
+                label="{label}",
+                atlas="{atlas}",
+                **config["subj_wildcards"]
+            ),
+            atlas=config["atlas"],
+            allow_missing=True,
+        ),
+        surfs=expand(
+            bids(
+                root=root,
+                datatype="surf",
+                den="{density}",
+                suffix="{surfname}.surf.gii",
+                space="{space}",
+                hemi="{hemi}",
+                label="{label}",
+                **config["subj_wildcards"]
+            ),
+            surfname=["midthickness"],
+            space=["{space}", "unfolded"],
+            allow_missing=True,
+        ),
+        cifti=lambda wildcards: expand(
+            bids(
+                root=root,
+                datatype="surf",
+                den="{density}",
+                suffix="{cifti}.nii",
+                space="{space}",
+                label="{label}",
+                **config["subj_wildcards"]
+            ),
+            cifti=get_cifti_metric_types(wildcards.label),
+            allow_missing=True,
+        ),
+    params:
+        cmds=get_cmd_spec_file,
+    output:
+        spec_file=bids(
+            root=root,
+            datatype="surf",
+            den="{density}",
+            suffix="surfaces.spec",
+            hemi="{hemi,L|R}",
+            space="{space}",
+            label="{label,hipp}",
+            **config["subj_wildcards"]
+        ),
+    container:
+        config["singularity"]["autotop"]
+    group:
+        "subj"
+    shell:
+        "{params.cmds}"
+
+
+rule create_spec_file_dentate:
     input:
         metrics=lambda wildcards: expand(
             bids(
@@ -722,7 +786,7 @@ rule create_spec_file:
                 label="{label}",
                 **config["subj_wildcards"]
             ),
-            metric=get_gifti_types(wildcards),
+            metric=get_gifti_metric_types(wildcards.label),
             allow_missing=True,
         ),
         surfs=expand(
@@ -750,7 +814,7 @@ rule create_spec_file:
                 label="{label}",
                 **config["subj_wildcards"]
             ),
-            cifti=get_cifti_types(wildcards),
+            cifti=get_cifti_metric_types(wildcards.label),
             allow_missing=True,
         ),
     params:
@@ -763,7 +827,7 @@ rule create_spec_file:
             suffix="surfaces.spec",
             hemi="{hemi,L|R}",
             space="{space}",
-            label="{label}",
+            label="{label,dentate}",
             **config["subj_wildcards"]
         ),
     container: