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khanlab · Dec 30, 2024 · 5ae5a8d · 5ae5a8d
1 parent 5accc40
commit 5ae5a8d
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Showing 9 changed files with 198 additions and 132 deletions.
diff --git a/hippunfold/resources/atlas-v2/Snakefile b/hippunfold/resources/atlas-v2/Snakefile
@@ -1,11 +1,10 @@
+hippunfold_dir = "/localscratch/hippunfold_khanlab"
+hipp_dseg = "sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz"
+labellist = "labellist_withdg.txt"
 
-hippunfold_dir='/localscratch/hippunfold_khanlab'
-hipp_dseg='sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz'
-labellist='labellist_withdg.txt'
-
-hemis=['L','R']
-metrics=['thickness','curvature','gyrification']
-surftypes=['midthickness','inner','outer']
+hemis = ["L", "R"]
+metrics = ["thickness", "curvature", "gyrification"]
+surftypes = ["midthickness", "inner", "outer"]
 
 hemi_to_structure = {"L": "CORTEX_LEFT", "R": "CORTEX_RIGHT"}
 surf_to_secondary_type = {
@@ -15,76 +14,93 @@ surf_to_secondary_type = {
 }
 
 
-
 rule all:
     input:
-        expand('hemi-{hemi}_label-{label}_dseg.label.gii',label=['hipp','dentate'],hemi=hemis),
-        expand('hemi-{hemi}_label-{label}_{metric}.shape.gii',label=['hipp'],hemi=hemis,metric=metrics),
-        expand('hemi-{hemi}_space-unfold_label-{label}_{surftype}.surf.gii',label=['hipp','dentate'],hemi=hemis,surftype=surftypes),
-
+        expand(
+            "hemi-{hemi}_label-{label}_dseg.label.gii",
+            label=["hipp", "dentate"],
+            hemi=hemis,
+        ),
+        expand(
+            "hemi-{hemi}_label-{label}_{metric}.shape.gii",
+            label=["hipp"],
+            hemi=hemis,
+            metric=metrics,
+        ),
+        expand(
+            "hemi-{hemi}_space-unfold_label-{label}_{surftype}.surf.gii",
+            label=["hipp", "dentate"],
+            hemi=hemis,
+            surftype=surftypes,
+        ),
 
 
 rule hipp_dseg:
     input:
-        hipp_dseg
+        hipp_dseg,
     output:
-        temp('hipp_dseg.nii.gz')
+        temp("hipp_dseg.nii.gz"),
     shell:
-        'cp {input} {output}'
+        "cp {input} {output}"
 
-rule dentate_dseg: 
+
+rule dentate_dseg:
     input:
-        hipp_dseg
+        hipp_dseg,
     params:
-        dg_label=6
+        dg_label=6,
     output:
-        temp('dentate_dseg.nii.gz')
+        temp("dentate_dseg.nii.gz"),
     shell:
-        'c3d {input} -scale 0 -shift {params.dg_label} -o {output}'
+        "c3d {input} -scale 0 -shift {params.dg_label} -o {output}"
+
 
 rule surf_gifti:
     input:
-        surf_gii=Path(hippunfold_dir) / 'hippunfold' / 'resources' / 'unfold_template_{label}' / 'tpl-avg_space-unfold_den-unfoldiso_{surftype}.surf.gii'
+        surf_gii=Path(hippunfold_dir)
+        / "hippunfold"
+        / "resources"
+        / "unfold_template_{label}"
+        / "tpl-avg_space-unfold_den-unfoldiso_{surftype}.surf.gii",
     params:
         structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi],
         secondary_type=lambda wildcards: surf_to_secondary_type[wildcards.surftype],
         surface_type="FLAT",
     output:
-        surf_gii='hemi-{hemi}_space-unfold_label-{label}_{surftype}.surf.gii'
+        surf_gii="hemi-{hemi}_space-unfold_label-{label}_{surftype}.surf.gii",
     shell:
-        'cp {input} {output} && '
+        "cp {input} {output} && "
         "wb_command -set-structure {output} {params.structure_type} -surface-type {params.surface_type}"
         " -surface-secondary-type {params.secondary_type}"
 
 
 rule label_gifti:
     input:
-        dseg_nii='{label}_dseg.nii.gz',
+        dseg_nii="{label}_dseg.nii.gz",
         lut=labellist,
-        surf_gii='hemi-{hemi}_space-unfold_label-{label}_midthickness.surf.gii'
+        surf_gii="hemi-{hemi}_space-unfold_label-{label}_midthickness.surf.gii",
     params:
         structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi],
     output:
-        label_gii='hemi-{hemi}_label-{label}_dseg.label.gii'
-    shadow: 'minimal'
+        label_gii="hemi-{hemi}_label-{label}_dseg.label.gii",
+    shadow:
+        "minimal"
     shell:
-        'wb_command -volume-label-import {input.dseg_nii} {input.lut} label_vol.nii && '
-        'wb_command -volume-label-to-surface-mapping label_vol.nii {input.surf_gii} {output.label_gii} && '
+        "wb_command -volume-label-import {input.dseg_nii} {input.lut} label_vol.nii && "
+        "wb_command -volume-label-to-surface-mapping label_vol.nii {input.surf_gii} {output.label_gii} && "
         "wb_command -set-structure {output} {params.structure_type}"
-
 
- 
+
 rule metric_gifti:
     input:
-        metric_nii='{metric}.nii.gz',
-        surf_gii='hemi-{hemi}_space-unfold_label-{label}_inner.surf.gii' #existing metric niftis are on inner space
+        metric_nii="{metric}.nii.gz",
+        surf_gii="hemi-{hemi}_space-unfold_label-{label}_inner.surf.gii",  #existing metric niftis are on inner space
     params:
         structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi],
     output:
-        metric_gii='hemi-{hemi}_label-{label}_{metric}.shape.gii'
-    shadow: 'minimal'
+        metric_gii="hemi-{hemi}_label-{label}_{metric}.shape.gii",
+    shadow:
+        "minimal"
     shell:
-        'wb_command -volume-to-surface-mapping {input.metric_nii} {input.surf_gii} {output.metric_gii} -trilinear && '
+        "wb_command -volume-to-surface-mapping {input.metric_nii} {input.surf_gii} {output.metric_gii} -trilinear && "
         "wb_command -set-structure {output} {params.structure_type}"
-
-
diff --git a/hippunfold/workflow/Snakefile b/hippunfold/workflow/Snakefile
@@ -168,6 +168,7 @@ else:
 
     include: "rules/shape_inject.smk"
 
+
 rule all:
     input:
         get_final_output(),

diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk
@@ -141,6 +141,7 @@ rule constrain_surf_to_bbox:
     script:
         "../scripts/constrain_surf_to_bbox.py"
 
+
 # needed for if native_modality is corobl
 rule cp_corobl_root:
     input:
@@ -214,6 +215,7 @@ rule affine_gii_to_native:
     shell:
         "wb_command -surface-apply-affine {input.gii} {input.xfm} {output.gii}"
 
+
 def get_cmd_cifti_metric(wildcards, input, output):
     cmd = f"wb_command  -cifti-create-dense-scalar {output}"
     if "L" in config["hemi"]:
@@ -370,6 +372,7 @@ def get_gifti_metric_types(label):
         types_list.append("myelin.shape")
     return types_list
 
+
 rule create_spec_file_hipp:
     input:
         metrics=lambda wildcards: expand(
@@ -413,7 +416,7 @@ rule create_spec_file_hipp:
                 **inputs.subj_wildcards
             ),
             surfname=["midthickness"],
-            space=["{space}", "unfold","unfoldreg"],
+            space=["{space}", "unfold", "unfoldreg"],
             allow_missing=True,
         ),
         cifti_metrics=lambda wildcards: inputs[config["modality"]].expand(
-Original file line number
+Diff line change
@@ Expand Up / @@ -168,6 +168,7 @@ else: @@
         include: "rules/shape_inject.smk"
     rule all:
         input:
             get_final_output(),
@@ Expand Down @@