deleted - Template-based segmentation, and new templates (marmoset, macaque)

hippunfold/config/snakebids.yml

@@ -128,7 +128,7 @@ parse_args:
   --version:
     help: 'Print the version of HippUnfold'
     action: version
-    version: "1.4.2-pre.34"
+    version: "1.4.2-pre.35"
 
 
   --modality:
@@ -141,7 +141,40 @@ parse_args:
       - segT1w
       - segT2w
       - cropseg
-
+
+
+  --template:
+    choices:
+      - 'CITI168'
+      - 'dHCP'
+      - 'MBMv2'
+      - 'MBMv3'
+      - 'CIVM'
+    default: 'CITI168'
+    help: 'Set the template to use for registration to coronal oblique (and optionally for template-based segmentation if --use-template-seg is enabled). CITI168 is for adult human data, dHCP is for neonatal human data, MBMv2 is for ex vivo marmoset data, MBMv3 is for in vivo marmoset data, and CIVM is for in vivo macaque data. (default: %(default)s)'
+
+
+
+
+  --inject_template:
+    choices:
+      - 'upenn'
+      - 'MBMv2'
+      - 'MBMv3'
+      - 'CIVM'
+    default: 'upenn'
+    help: 'Set the template to use for shape injection. (default: %(default)s)'
+
+  --use_template_seg:
+    help: 'Use template-based segmentation for hippocampal tissue *instead of* nnUnet and shape injection. This is only to be used if nnUnet models are not trained for the data you are using, e.g. for non-human primate data with the MBMv2 (ex vivo marmoset), MBMv3 (in vivomarmoset), or CIVM (in vivo macaque) template. (default: %(default)s)'
+    default: False
+    action: 'store_true'
+
+  --template_seg_smoothing_factor: 
+    help: 'Scales the default smoothing sigma for gradient and warp in greedy registration for template-based segmentation. Using a value higher than 1 will use result in a smoother warp. (default: %(default)s)'
+    default: 2.0
+
+
   --derivatives:
     help: 'Path to the derivatives folder (e.g. for finding manual segs) (default: %(default)s) '
     default: False
@@ -178,13 +211,7 @@ parse_args:
     default: False
     action: 'store_true'
 
-  --template:
-    choices:
-      - 'CITI168'
-      - 'dHCP'
-    default: 'CITI168'
-    help: 'Set the template to use for registration to coronal oblique. (default: %(default)s)'
-
+
   --t1_reg_template:
     help: 'Use T1w to register to template space, instead of the segmentation modality. Note: this was the default behavior prior to v1.0.0.  (default: %(default)s)'
     default: false
@@ -354,6 +381,33 @@ template_files:
     crop_ref: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_T2w.nii.gz
     crop_refT1w: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_T1w.nii.gz
     Mask_crop: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_desc-hipp_mask.nii.gz
+  MBMv2:
+    T1w: Template_sym_MTR_80um.nii.gz
+    T2w: Template_sym_T2_80um.nii.gz
+    xfm_corobl: tpl-MBMv2_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: tpl-MBMv2_hemi-{hemi}_space-corobl_{modality}.nii.gz
+    Mask_crop: tpl-MBMv2_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
+    dseg: tpl-MBMv2_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
+    coords: tpl-MBMv2_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+  MBMv3:
+    T1w: tpl-MBMv3_T1w.nii.gz
+    T2w: tpl-MBMv3_T2w.nii.gz
+    xfm_corobl: tpl-MBMv3_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: tpl-MBMv3_hemi-{hemi}_space-corobl_{modality}.nii.gz
+    Mask_crop: tpl-MBMv3_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
+    dseg: tpl-MBMv3_hemi-R_space-corobl_desc-tissue_dseg.nii.gz
+    coords: tpl-MBMv3_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+  CIVM:
+    T1w: tpl-CIVM_T1w.nii.gz
+    xfm_corobl: tpl-CIVM_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: tpl-CIVM_hemi-{hemi}_space-corobl_{modality}.nii.gz
+    Mask_crop: tpl-CIVM_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
+    dseg: tpl-CIVM_hemi-R_space-corobl_desc-tissue_dseg.nii.gz
+    coords: tpl-CIVM_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+  upenn:
+    T1w: tpl-upenn_desc-hipptissue_dseg.nii.gz
+    dseg: tpl-upenn_desc-hipptissue_dseg.nii.gz
+    coords: tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
 
 atlas_files:
   multihist7:
@@ -404,6 +458,8 @@ no_reg_template: False
 
 modality: T2w
 
+inject_template: upenn
+
 template: CITI168
 
 atlas: 
@@ -572,3 +628,5 @@ t1_reg_template: False
 generate_myelin_map: False
 no_unfolded_reg: False
 root: results
+use_template_seg: False
+template_seg_smoothing_factor: 2

hippunfold/pipeline_description.json

@@ -5,7 +5,7 @@
     "GeneratedBy": [
         {
             "Name": "hippunfold",
-            "Version": "1.4.2-pre.34",
+            "Version": "1.4.2-pre.35",
             "CodeURL": "https://github.com/khanlab/hippunfold",
             "Author": "Jordan DeKraker & Ali Khan",
             "AuthorEmail": "ali.khan@uwo.ca"

hippunfold/workflow/Snakefile

@@ -59,7 +59,7 @@ elif "T1w" in config["modality"]:
 
 # only generate hipp surface if skipping template injection
 #   i.e. drop dentate
-if config["skip_inject_template_labels"]:
+if config["skip_inject_template_labels"]:  # TODO do we need this?
     config["autotop_labels"] = ["hipp"]
 
 
@@ -144,9 +144,6 @@ include: "rules/autotop.smk"
 include: "rules/warps.smk"
 
 
-include: "rules/shape_inject.smk"
-
-
 include: "rules/gifti.smk"
 
 
@@ -162,6 +159,26 @@ include: "rules/qc.smk"
 include: "rules/myelin_map.smk"
 
 
+if config["use_template_seg"]:
+    if (
+        "dseg" in config["template_files"][config["template"]]
+        and "coords" in config["template_files"][config["template"]]
+    ):
+
+        include: "rules/templateseg.smk"
+
+    else:
+        print(
+            "use_template_seg is not possible, template dseg or coords do not exist for the chosen template"
+        )
+
+        include: "rules/shape_inject.smk"
+
+else:
+
+    include: "rules/shape_inject.smk"
+
+
 rule all:
     input:
         get_final_output(),

hippunfold/workflow/rules/common.smk

@@ -293,20 +293,21 @@ def get_final_qc():
             )
         )
     if (config["modality"] == "T1w") or (config["modality"] == "T2w"):
-        qc.extend(
-            expand(
-                bids(
-                    root=root,
-                    datatype="qc",
-                    desc="unetf3d",
-                    suffix="dice.tsv",
-                    hemi="{hemi}",
-                    **config["subj_wildcards"],
-                ),
-                hemi=config["hemi"],
-                allow_missing=True,
+        if not config["use_template_seg"]:
+            qc.extend(
+                expand(
+                    bids(
+                        root=root,
+                        datatype="qc",
+                        desc="unetf3d",
+                        suffix="dice.tsv",
+                        hemi="{hemi}",
+                        **config["subj_wildcards"],
+                    ),
+                    hemi=config["hemi"],
+                    allow_missing=True,
+                )
             )
-        )
     return qc
 
 

hippunfold/workflow/rules/gifti.smk

@@ -466,7 +466,7 @@ rule metric_to_nii:
     params:
         interp="-nearest-vertex 1",
         refflatnii=lambda wildcards, input: Path(input.atlas_dir)
-        / config["atlas_files"]["multihist7"]["label_nii"],
+        / config["atlas_files"]["multihist7"]["label_nii"].format(**wildcards),
     output:
         metric_nii=bids(
             root=work,
@@ -531,11 +531,11 @@ rule unfolded_registration:
         warpfn="tmp1Warp.nii.gz",
         invwarpfn="tmp1InverseWarp.nii.gz",
         refthickness=lambda wildcards, input: Path(input.atlas_dir)
-        / config["atlas_files"][wildcards.atlas]["thickness"],
+        / config["atlas_files"][wildcards.atlas]["thickness"].format(**wildcards),
         refcurvature=lambda wildcards, input: Path(input.atlas_dir)
-        / config["atlas_files"][wildcards.atlas]["curvature"],
+        / config["atlas_files"][wildcards.atlas]["curvature"].format(**wildcards),
         refgyrification=lambda wildcards, input: Path(input.atlas_dir)
-        / config["atlas_files"][wildcards.atlas]["gyrification"],
+        / config["atlas_files"][wildcards.atlas]["gyrification"].format(**wildcards),
     output:
         warp=bids(
             root=work,
@@ -1058,7 +1058,7 @@ rule resample_atlas_to_refvol:
         atlas_dir=lambda wildcards: Path(download_dir) / "atlas" / wildcards.atlas,
     params:
         atlas=lambda wildcards, input: Path(input.atlas_dir)
-        / config["atlas_files"][wildcards.atlas]["label_nii"],
+        / config["atlas_files"][wildcards.atlas]["label_nii"].format(**wildcards),
     output:
         label_nii=bids(
             root=work,
@@ -1110,7 +1110,7 @@ rule nii_to_label_gii:
         atlas_dir=lambda wildcards: Path(download_dir) / "atlas" / wildcards.atlas,
     params:
         label_list=lambda wildcards, input: Path(input.atlas_dir)
-        / config["atlas_files"][wildcards.atlas]["label_list"],
+        / config["atlas_files"][wildcards.atlas]["label_list"].format(**wildcards),
         structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi],
     output:
         label_gii=bids(
@@ -1131,7 +1131,7 @@ rule nii_to_label_gii:
     shadow:
         "minimal"
     shell:
-        "wb_command -volume-to-surface-mapping {params.label_list} {input.surf} temp.shape.gii -enclosing  && "
+        "wb_command -volume-to-surface-mapping {input.label_nii} {input.surf} temp.shape.gii -enclosing  && "
         "wb_command -metric-label-import temp.shape.gii {params.label_list} {output.label_gii} && "
         "wb_command -set-structure {output.label_gii} {params.structure_type}"
 

hippunfold/workflow/rules/nnunet.smk

@@ -203,15 +203,13 @@ rule unflip_nnunet_nii:
 def get_f3d_ref(wildcards, input):
 
     if config["modality"] == "T2w":
-        nii = (
-            Path(input.template_dir)
-            / config["template_files"][config["template"]]["crop_ref"]
-        )
+        nii = Path(input.template_dir) / config["template_files"][config["template"]][
+            "crop_ref"
+        ].format(**wildcards)
     elif config["modality"] == "T1w":
-        nii = (
-            Path(input.template_dir)
-            / config["template_files"][config["template"]]["crop_refT1w"]
-        )
+        nii = Path(input.template_dir) / config["template_files"][config["template"]][
+            "crop_refT1w"
+        ].format(**wildcards)
     else:
         raise ValueError("modality not supported for nnunet!")
     return nii
@@ -302,8 +300,12 @@ rule qc_nnunet_dice:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         hipp_lbls=[1, 2, 7, 8],
-        ref=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["Mask_crop"],
+        ref=lambda wildcards, input: (
+            Path(input.template_dir)
+            / config["template_files"][config["template"]]["Mask_crop"].format(
+                **wildcards
+            )
+        ),
     output:
         dice=report(
             bids(

hippunfold/workflow/rules/preproc_seg.smk

@@ -42,7 +42,7 @@ rule warp_seg_to_corobl_crop:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         ref=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["crop_ref"],
+        / config["template_files"][config["template"]]["crop_ref"].format(**wildcards),
     output:
         nii=bids(
             root=work,

hippunfold/workflow/rules/preproc_t1.smk

@@ -72,9 +72,11 @@ else:
 
 def reg_to_template_cmd(wildcards, input, output):
 
-    ref = (
+    ref = str(
         Path(input.template_dir)
-        / config["template_files"][config["template"]][wildcards.modality],
+        / config["template_files"][config["template"]][wildcards.modality].format(
+            **wildcards
+        ),
     )
     if config["no_reg_template"]:
         cmd = f"reg_resample -flo {input.flo} -ref {ref} -res {output.warped_subj} -aff {input.xfm_identity}; cp {input.xfm_identity} {output.xfm_ras}"
@@ -183,7 +185,9 @@ rule compose_template_xfm_corobl:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         std_to_cor=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["xfm_corobl"],
+        / config["template_files"][config["template"]]["xfm_corobl"].format(
+            **wildcards
+        ),
     output:
         sub_to_cor=bids(
             root=work,
@@ -241,7 +245,7 @@ rule template_xfm_itk2ras:
             datatype="warps",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="{native_modality,T1w|T2w}",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="itk"
@@ -288,7 +292,7 @@ rule warp_t1_to_corobl_crop:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         ref=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["crop_ref"],
+        / config["template_files"][config["template"]]["crop_ref"].format(**wildcards),
     output:
         t1=bids(
             root=work,

hippunfold/workflow/rules/preproc_t2.smk

@@ -308,10 +308,9 @@ def get_cmd_compose_t2_xfm_corobl(wildcards, input):
         # xfm0: t2 to template
         xfm0 = input.t2_to_std
         # xfm1: template to corobl
-        xfm1 = (
-            Path(input.template_dir)
-            / config["template_files"][config["template"]]["xfm_corobl"]
-        )
+        xfm1 = Path(input.template_dir) / config["template_files"][config["template"]][
+            "xfm_corobl"
+        ].format(**wildcards)
 
     return "c3d_affine_tool -itk {xfm0} -itk {xfm1} -mult -oitk {output}"
 
@@ -394,7 +393,7 @@ rule warp_t2_to_corobl_crop:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         ref=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["crop_ref"],
+        / config["template_files"][config["template"]]["crop_ref"].format(**wildcards),
     output:
         nii=bids(
             root=work,

hippunfold/workflow/rules/qc.smk

@@ -10,8 +10,12 @@ rule qc_reg_to_template:
         ),
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
-        ref=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]][wildcards.native_modality],
+        ref=lambda wildcards, input: str(
+            Path(input.template_dir)
+            / config["template_files"][config["template"]][
+                wildcards.native_modality
+            ].format(**wildcards)
+        ),
     output:
         png=report(
             bids(