Fixes to get this branch working

- had some conflicts to resolve from the atlas PRs - working with dry-run now - TODO: full test, and consider making surf metrics consistent with volume tsv files in format/layout -- or maybe an additional single tidy table for all
khanlab · Aug 15, 2022 · 58e395c · 58e395c
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diff --git a/...ces/bigbrain/sub-bigbrain_labellist.L.txt → ...sources/bigbrain/bigbrain_labellist.L.txt b/...ces/bigbrain/sub-bigbrain_labellist.L.txt → ...sources/bigbrain/bigbrain_labellist.L.txt
diff --git a/...ces/bigbrain/sub-bigbrain_labellist.R.txt → ...sources/bigbrain/bigbrain_labellist.R.txt b/...ces/bigbrain/sub-bigbrain_labellist.R.txt → ...sources/bigbrain/bigbrain_labellist.R.txt
diff --git a/hippunfold/resources/freesurfer/freesurfer_labellist.L.txt b/hippunfold/resources/freesurfer/freesurfer_labellist.L.txt
@@ -0,0 +1,88 @@
+Left alveus
+201 255 204 153 255
+Left perforant_pathway
+202 255 128 128 255
+Left parasubiculum
+203 175 175 75  255
+Left presubiculum
+204 64  0   64  255
+Left subiculum
+205 0   0   255 255
+Left CA1
+206 255 0   0   255
+Left CA2
+207 128 128 255 255
+Left CA3
+208 0   128 0   255
+Left CA4
+209 196 160 128 255
+Left GC-DG
+210 32  200 255 255
+Left HATA
+211 128 255 128 255
+Left fimbria
+212 204 153 204 255
+Left lateral_ventricle
+213 121 17  136 255
+Left molecular_layer_HP
+214 128 0   0   255
+Left hippocampal_fissure
+215 128 32  255 255
+Left entorhinal_cortex
+216 255 204 102 255
+Left molecular_layer_subiculum
+217 128 128 128 255
+Left Amygdala
+218 104 255 255 255
+Left Cerebral_White_Matter
+219 0   226 0   255
+Left Cerebral_Cortex
+220 205 63  78  255
+Left Inf_Lat_Vent
+221 197 58  250 255
+Left Perirhinal
+222 33  150 250 255
+Left Cerebral_White_Matter_Edge
+223 226 0   0   255
+Left Background
+224 100 100 100 255
+Left Ectorhinal
+225 197 150 250 255
+Left HP_tail
+226 170 170 255 255
+Left Polymorphic-Layer
+227 128 255 128 255
+Left Intracellular-Space
+228 204 153 204 255
+Left HP_body
+231 0 255 0 255
+Left HP_head
+232 255 0 0 255
+Left presubiculum-head
+233 32  0   32  255
+Left presubiculum-body
+234 64  0   64  255
+Left subiculum-head
+235 0   0   175 255
+Left subiculum-body
+236 0   0   255 255
+Left CA1-head
+237 175 75   75   255
+Left CA1-body
+238 255 0   0   255
+Left CA3-head
+239 0   80 0   255
+Left CA3-body
+240 0   128 0   255
+Left CA4-head
+241 120 90 50 255
+Left CA4-body
+242 196 160 128 255
+Left GC-ML-DG-head
+243 75   125 175 255
+Left GC-ML-DG-body
+244 32  200 255 255
+Left molecular_layer_HP-head
+245 100 25   25   255
+Left molecular_layer_HP-body
+246 128 0   0   255
diff --git a/hippunfold/resources/freesurfer/freesurfer_labellist.R.txt b/hippunfold/resources/freesurfer/freesurfer_labellist.R.txt
@@ -0,0 +1,88 @@
+Right alveus
+201 255 204 153 255
+Right perforant_pathway
+202 255 128 128 255
+Right parasubiculum
+203 175 175 75  255
+Right presubiculum
+204 64  0   64  255
+Right subiculum
+205 0   0   255 255
+Right CA1
+206 255 0   0   255
+Right CA2
+207 128 128 255 255
+Right CA3
+208 0   128 0   255
+Right CA4
+209 196 160 128 255
+Right GC-DG
+210 32  200 255 255
+Right HATA
+211 128 255 128 255
+Right fimbria
+212 204 153 204 255
+Right lateral_ventricle
+213 121 17  136 255
+Right molecular_layer_HP
+214 128 0   0   255
+Right hippocampal_fissure
+215 128 32  255 255
+Right entorhinal_cortex
+216 255 204 102 255
+Right molecular_layer_subiculum
+217 128 128 128 255
+Right Amygdala
+218 104 255 255 255
+Right Cerebral_White_Matter
+219 0   226 0   255
+Right Cerebral_Cortex
+220 205 63  78  255
+Right Inf_Lat_Vent
+221 197 58  250 255
+Right Perirhinal
+222 33  150 250 255
+Right Cerebral_White_Matter_Edge
+223 226 0   0   255
+Right Background
+224 100 100 100 255
+Right Ectorhinal
+225 197 150 250 255
+Right HP_tail
+226 170 170 255 255
+Right Polymorphic-Layer
+227 128 255 128 255
+Right Intracellular-Space
+228 204 153 204 255
+Right HP_body
+231 0 255 0 255
+Right HP_head
+232 255 0 0 255
+Right presubiculum-head
+233 32  0   32  255
+Right presubiculum-body
+234 64  0   64  255
+Right subiculum-head
+235 0   0   175 255
+Right subiculum-body
+236 0   0   255 255
+Right CA1-head
+237 175 75   75   255
+Right CA1-body
+238 255 0   0   255
+Right CA3-head
+239 0   80 0   255
+Right CA3-body
+240 0   128 0   255
+Right CA4-head
+241 120 90 50 255
+Right CA4-body
+242 196 160 128 255
+Right GC-ML-DG-head
+243 75   125 175 255
+Right GC-ML-DG-body
+244 32  200 255 255
+Right molecular_layer_HP-head
+245 100 25   25   255
+Right molecular_layer_HP-body
+246 128 0   0   255
diff --git a/hippunfold/resources/magdeburg/magdeburg_labellist.L.txt b/hippunfold/resources/magdeburg/magdeburg_labellist.L.txt
@@ -0,0 +1,28 @@
+Left CA1
+1 255 0 0 255
+Left CA2 
+2 0 255 0 255
+Left DG 
+3 0 0 255 255
+Left CA3
+4 255 255 0 255
+Left Tail
+5 0 255 255 255
+Left Label_6
+6 255 0 255 255
+Left Label_7
+7 255 239 213 255
+Left Sub
+8 240 86 224 255
+Left ErC
+9 205 133 63 255
+Left A35
+10 102 205 170 255
+Left A36
+11 0 0 128 255
+Left PhC
+12 230 0 50 255
+Left Cysts
+13 55 160 230 255
+Left Label_17
+17 221 160 221 255
diff --git a/hippunfold/resources/magdeburg/magdeburg_labellist.R.txt b/hippunfold/resources/magdeburg/magdeburg_labellist.R.txt
@@ -0,0 +1,28 @@
+Right CA1
+1 255 0 0 255
+Right CA2 
+2 0 255 0 255
+Right DG 
+3 0 0 255 255
+Right CA3
+4 255 255 0 255
+Right Tail
+5 0 255 255 255
+Right Label_6
+6 255 0 255 255
+Right Label_7
+7 255 239 213 255
+Right Sub
+8 240 86 224 255
+Right ErC
+9 205 133 63 255
+Right A35
+10 102 205 170 255
+Right A36
+11 0 0 128 255
+Right PhC
+12 230 0 50 255
+Right Cysts
+13 55 160 230 255
+Right Label_17
+17 221 160 221 255
diff --git a/hippunfold/workflow/rules/common.smk b/hippunfold/workflow/rules/common.smk
@@ -301,10 +301,12 @@ def get_final_qc():
                     space="{space}",
                     suffix="{metric}.png",
                     den="{density}",
+                    atlas="{atlas}",
                     **config["subj_wildcards"],
                 ),
                 density=config["output_density"],
                 metric=["gyrification", "curvature", "thickness"],
+                atlas=config["atlas"],
                 space=ref_spaces,
                 allow_missing=True,
             )

diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk
@@ -516,44 +516,6 @@ rule nii_to_label_gii:
             "unfold_template_hipp",
             "tpl-avg_space-unfold_den-{density}_midthickness.surf.gii",
         ),
-    output:
-        metric_gii=bids(
-            root=work,
-            datatype="surf",
-            den="{density}",
-            suffix="subfields.label.func.gii",
-            space="{space}",
-            hemi="{hemi}",
-            label="hipp",
-            **config["subj_wildcards"]
-        ),
-    group:
-        "subj"
-    container:
-        config["singularity"]["autotop"]
-    shell:
-        "wb_command -metric-convert -from-nifti {input.label_nii} {input.surf} {output.metric_gii}"
-
-
-rule metric_to_label_gii:
-    input:
-        metric_gii=bids(
-            root=work,
-            datatype="surf",
-            den="{density}",
-            suffix="subfields.label.func.gii",
-            space="{space}",
-            hemi="{hemi}",
-            label="hipp",
-            **config["subj_wildcards"]
-        ),
-        label_list=os.path.join(
-            workflow.basedir,
-            "..",
-            "resources",
-            "bigbrain",
-            "sub-bigbrain_labellist.{hemi}.txt",
-        ),
     output:
         label_gii=bids(
             root=root,
@@ -574,6 +536,10 @@ rule metric_to_label_gii:
         "wb_command -volume-to-surface-mapping {input.label_nii} {input.surf} {output.label_gii} -enclosing"
 
 
+
+
+
+
 def get_cmd_cifti_metric(wildcards, input, output):
     cmd = f"wb_command  -cifti-create-dense-scalar {output}"
     if "L" in config["hemi"]:
@@ -919,6 +885,7 @@ rule create_parcellated_scalar_csv:
             suffix="subfields.dlabel.nii",
             space="{space}",
             label="hipp",
+            atlas="{atlas}",
             **config["subj_wildcards"]
         ),
         dscalar=bids(
@@ -938,6 +905,7 @@ rule create_parcellated_scalar_csv:
             suffix="{metric}.csv",
             space="{space}",
             label="{autotop,hipp}",
+            atlas="{atlas}",
             **config["subj_wildcards"]
         ),
     container:

diff --git a/hippunfold/workflow/rules/qc.smk b/hippunfold/workflow/rules/qc.smk
@@ -269,6 +269,7 @@ rule plot_subj_surf_scalars:
             suffix="{metric}.csv",
             space="{space}",
             label="hipp",
+            atlas="{atlas}",
             **config["subj_wildcards"]
         ),
     output:
@@ -280,6 +281,7 @@ rule plot_subj_surf_scalars:
                 den="{density}",
                 desc="subfields",
                 suffix="{metric}.png",
+                atlas="{atlas}",
                 **config["subj_wildcards"]
             ),
         ),