bugfix: subfield+tissue for new atlases, and tsv files

hippunfold/config/snakebids.yml

@@ -345,6 +345,28 @@ atlas_files:
     label_list: resources/freesurfer/freesurfer_labellist.txt
 
 
+#values to use for re-mapping tissue labels when combining with subfields.
+# set the SRLM and Cyst labels to always be higher than any label in the atlas (so they override)
+tissue_atlas_mapping:
+  tissue:
+    dg: 8
+    srlm: 2
+    cyst: 7
+  bigbrain:
+    dg: 6
+    srlm: 7
+    cyst: 8
+  magdeburg:
+    dg: 3
+    srlm: 9
+    cyst: 10
+  freesurfer:
+    dg: 209
+    srlm: 227
+    cyst: 228
+
+
+
 rigid_reg_template: False
 no_reg_template: False
 

hippunfold/resources/desc-subfields_atlas-bigbrain_dseg.tsv

@@ -0,0 +1,9 @@
+index	name	abbreviation
+1	subiculum	Sub
+2	CA1	CA1
+3	CA2	CA2
+4	CA3	CA3
+5	CA4	CA4
+6	dentate gyrus	DG
+7	SRLM or 'dark band'	SRLM
+8	cysts	Cyst

hippunfold/resources/desc-subfields_atlas-freesurfer_dseg.tsv

@@ -0,0 +1,10 @@
+index	name	abbreviation
+203	parasubiculum	ParaSub
+204	presubiculum	PreSub
+205	subiculum	Sub
+206	CA1	CA1
+208	CA3	CA3
+209	CA4 and dentate gyrus	CA4_DG
+226	tail	Tail
+227	SRLM or 'dark band'	SRLM
+228	cysts	Cyst

hippunfold/resources/desc-subfields_atlas-magdeburg_dseg.tsv

@@ -0,0 +1,9 @@
+index	name	abbreviation
+1	CA1	CA1
+2	CA2	CA2
+3	dentate gyrus	DG
+4	CA3	CA3
+5	tail	Tail
+8	subiculum	Sub
+9	SRLM or 'dark band'	SRLM
+10	cysts	Cyst

hippunfold/workflow/rules/qc.smk

@@ -50,7 +50,10 @@ rule get_subfield_vols_subj:
             allow_missing=True,
         ),
         lookup_tsv=os.path.join(
-            workflow.basedir, "..", "resources", "desc-subfields_dseg.tsv"
+            workflow.basedir,
+            "..",
+            "resources",
+            "desc-subfields_atlas-{atlas}_dseg.tsv",
         ),
     group:
         "subj"

hippunfold/workflow/rules/subfields.smk

@@ -52,13 +52,25 @@ rule label_subfields_from_vol_coords_corobl:
         "../scripts/label_subfields_from_vol_coords.py"
 
 
+def get_tissue_atlas_remapping(wildcards):
+
+    mapping = config["tissue_atlas_mapping"]
+
+    remap = []
+
+    for label in mapping["tissue"].keys():
+        in_label = mapping["tissue"][label]
+        out_label = mapping[wildcards.atlas][label]
+
+        remap.append(f"-threshold {in_label} {in_label} {out_label} 0 -popas {label}")
+
+    return " ".join(remap)
+
+
 rule combine_tissue_subfield_labels_corobl:
     """Combine subfield labels with the DG, SRLM and Cyst tissue labels
 
     add srlm, cyst, dg from postproc labels to subfields
-    input dg label 8, output 6
-    input srlm label 2, output 7
-    input cyst label 7, output 8
 
     first remap tissue labels to get three sep labels
     then, we just need to add those in, using max(old,new) to override old with new in case of conflict
@@ -76,9 +88,7 @@ rule combine_tissue_subfield_labels_corobl:
             **config["subj_wildcards"]
         ),
     params:
-        remap_dg="-threshold 8 8 6 0 -popas dg",
-        remap_srlm="-threshold 2 2 7 0 -popas srlm",
-        remap_cyst="-threshold 7 7 8 0 -popas cyst",
+        remap=get_tissue_atlas_remapping,
     output:
         combined=bids(
             root=work,
@@ -95,7 +105,7 @@ rule combine_tissue_subfield_labels_corobl:
     group:
         "subj"
     shell:
-        "c3d {input.tissue} -dup {params.remap_dg} -dup {params.remap_srlm} {params.remap_cyst} {input.subfields} -push dg -max -push srlm -max -push cyst -max -type uchar -o {output}"
+        "c3d {input.tissue} -dup -dup {params.remap} {input.subfields} -push dg -max -push srlm -max -push cyst -max -type uchar -o {output}"
 
 
 rule resample_subfields_to_native: