Simple lflip (#335)

* initial atempt, not yet wetrun tested * lint * moved redundant rules to downloads.smk * lint * a bit more brevity * copy or flip instead of copy then flip * minor fixed to BBtemplate from wetrun testing * this refactors the config to put template stuff together - adds a hemi_wildcards field instead --------- Co-authored-by: Jordan DeKraker <[email protected]> Co-authored-by: Ali Khan <[email protected]>
khanlab · Dec 19, 2024 · 3d0a60c · 3d0a60c
1 parent ca08e47
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diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
@@ -354,41 +354,7 @@ singularity:
 xfm_identity: resources/etc/identity_xfm.txt
 xfm_identity_itk: resources/etc/identity_xfm_itk.txt
 
-#templates enabled for template-based segmentation are here
 # TODO: should also perhaps include modalities avaialble, and any custom crop_native_res settings
-template_based_segmentation:
-  CITI168:
-    hemi:
-      - R
-      - L
-  dHCP:
-    hemi:
-      - R
-      - L
-
-  MBMv2:
-    hemi:
-      - R
-  MBMv3:
-    hemi:
-      - R
-  CIVM:
-    hemi:
-      - R
-      - L
-  upenn:
-    hemi:
-      - R
-  ABAv3:
-    hemi:
-      - R
-      - L
-  bigbrain:
-    hemi:
-      - R
-      - L
-
-
 template_files:
   CITI168:
     T1w: T1w_head_700um.nii.gz
@@ -399,6 +365,9 @@ template_files:
     Mask_crop: Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
     dseg:  sub-CITI168_hemi-{hemi}_space-cropT1w_desc-postproc_dseg.nii.gz 
     coords: sub-CITI168_dir-{dir}_hemi-{hemi}_space-cropT1w_label-{autotop}_desc-laplace_coords.nii.gz 
+    hemi_wildcards:
+      - L
+      - R
   dHCP:
     T1w: tpl-dHCP_cohort-1_res-1_T1w.nii.gz
     T2w: tpl-dHCP_cohort-1_res-1_T2w.nii.gz
@@ -408,6 +377,10 @@ template_files:
     Mask_crop: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_desc-hipp_mask.nii.gz
     dseg: tpl-dHCP_space-corobl_hemi-{hemi}_desc-tissuemanualseg_dseg.nii.gz
     coords: tpl-dHCP_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+    hemi_wildcards:
+      - L
+      - R
+
   MBMv2:
     T1w: Template_sym_MTR_80um.nii.gz
     T2w: Template_sym_T2_80um.nii.gz
@@ -416,6 +389,9 @@ template_files:
     Mask_crop: tpl-MBMv2_hemi-R_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
+    hemi_wildcards:
+      - R
+
   MBMv3:
     T1w: tpl-MBMv3_T1w.nii.gz
     T2w: tpl-MBMv3_T2w.nii.gz
@@ -424,24 +400,40 @@ template_files:
     Mask_crop: tpl-MBMv3_hemi-R_space-corobl_desc-hipp_mask.nii.gz
     dseg: tpl-MBMv3_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
     coords: tpl-MBMv3_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+    hemi_wildcards:
+      - R
+
+
   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-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz
     coords: tpl-CIVM_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+    hemi_wildcards:
+      - L
+      - R
+
+
   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
+    hemi_wildcards:
+      - R
+
   ABAv3:
     T1w: tpl-ABAv3_T1w.nii.gz
     xfm_corobl: tpl-ABAv3_from-native_to-corobl_type-itk_affine.txt
     crop_ref: tpl-ABAv3_hemi-{hemi}_space-corobl_T1w.nii.gz
     Mask_crop: tpl-ABAv3_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz
     dseg: tpl-ABAv3_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz
     coords: tpl-ABAv3_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+    hemi_wildcards:
+      - L
+      - R
+
   bigbrain:
     T1w: tpl-bigbrain_1mm_merker.nii.gz
     T2w: tpl-bigbrain_1mm_merker.nii.gz
@@ -450,6 +442,10 @@ template_files:
     Mask_crop: tpl-bigbrain_hemi-{hemi}_space-corobl_desc-tissuemanual_100um_dseg.nii.gz
     dseg: tpl-bigbrain_hemi-{hemi}_space-corobl_desc-tissuemanual_100um_dseg.nii.gz
     coords: tpl-bigbrain_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+    hemi_wildcards:
+      - L
+      - R
+
 
 
 atlas_files:

diff --git a/hippunfold/workflow/rules/download.smk b/hippunfold/workflow/rules/download.smk
@@ -29,3 +29,134 @@ rule download_extract_template:
     shell:
         "wget https://{params.url} -O temp.zip && "
         " unzip -d {output.unzip_dir} temp.zip"
+
+
+## unpack template
+# this is used in both shape_inject.smk and templateseg.smk, so instead of having redundant rules I will simply apply them hemisphere
+# Template-based segmentation supports templates that have only a single hemisphere
+# by flipping it
+
+
+def copy_or_flip(wildcards, file_to_process):
+    if (
+        wildcards.hemi
+        in config["template_files"][config["inject_template"]]["hemi_wildcards"]
+    ):
+        cmd = f"cp {file_to_process}"
+    else:
+        cmd = f"c3d {file_to_process} -flip x -o"
+    return cmd
+
+
+rule import_template_dseg:
+    input:
+        template_dir=Path(download_dir) / "template" / config["inject_template"],
+    params:
+        template_seg=lambda wildcards: Path(download_dir)
+        / "template"
+        / config["inject_template"]
+        / config["template_files"][config["inject_template"]]["dseg"].format(
+            **wildcards
+        ),
+        copy_or_flip_cmd=lambda wildcards: copy_or_flip(
+            wildcards,
+            Path(download_dir)
+            / "template"
+            / config["inject_template"]
+            / config["template_files"][config["inject_template"]]["dseg"].format(
+                **wildcards
+            ),
+        ),
+    output:
+        template_seg=bids(
+            root=work,
+            datatype="anat",
+            space="template",
+            **inputs.subj_wildcards,
+            desc="hipptissue",
+            hemi="{hemi}",
+            suffix="dseg.nii.gz"
+        ),
+    group:
+        "subj"
+    container:
+        config["singularity"]["autotop"]
+    shell:
+        "{params.copy_or_flip_cmd} {output.template_seg}"
+
+
+rule import_template_coords:
+    input:
+        template_dir=Path(download_dir) / "template" / config["inject_template"],
+    params:
+        template_coords=lambda wildcards: Path(download_dir)
+        / "template"
+        / config["inject_template"]
+        / config["template_files"][config["inject_template"]]["coords"].format(
+            **wildcards
+        ),
+        copy_or_flip_cmd=lambda wildcards: copy_or_flip(
+            wildcards,
+            Path(download_dir)
+            / "template"
+            / config["inject_template"]
+            / config["template_files"][config["inject_template"]]["coords"].format(
+                **wildcards
+            ),
+        ),
+    output:
+        template_coords=bids(
+            root=work,
+            datatype="coords",
+            **inputs.subj_wildcards,
+            dir="{dir}",
+            label="{autotop}",
+            suffix="coords.nii.gz",
+            desc="init",
+            space="template",
+            hemi="{hemi}",
+        ),
+    group:
+        "subj"
+    container:
+        config["singularity"]["autotop"]
+    shell:
+        "{params.copy_or_flip_cmd} {output.template_coords}"
+
+
+rule import_template_anat:
+    input:
+        template_dir=Path(download_dir) / "template" / config["inject_template"],
+    params:
+        template_anat=lambda wildcards: Path(download_dir)
+        / "template"
+        / config["inject_template"]
+        / config["template_files"][config["inject_template"]][
+            get_modality_suffix(config["modality"])
+        ].format(**wildcards),
+        copy_or_flip_cmd=lambda wildcards: copy_or_flip(
+            wildcards,
+            Path(download_dir)
+            / "template"
+            / config["inject_template"]
+            / config["template_files"][config["inject_template"]][
+                get_modality_suffix(config["modality"])
+            ].format(**wildcards),
+        ),
+    output:
+        template_anat=bids(
+            root=work,
+            datatype="anat",
+            space="template",
+            **inputs.subj_wildcards,
+            hemi="{hemi}",
+            suffix="{modality}.nii.gz".format(
+                modality=get_modality_suffix(config["modality"])
+            ),
+        ),
+    group:
+        "subj"
+    container:
+        config["singularity"]["autotop"]
+    shell:
+        "{params.copy_or_flip_cmd} {output.template_anat}"
diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk
@@ -1,5 +1,5 @@
 # lookup tables for structure:
-hemi_to_structure = {"L": "CORTEX_LEFT", "Lflip": "CORTEX_LEFT", "R": "CORTEX_RIGHT"}
+hemi_to_structure = {"L": "CORTEX_LEFT", "R": "CORTEX_RIGHT"}
 surf_to_secondary_type = {
     "midthickness": "MIDTHICKNESS",
     "inner": "PIAL",

diff --git a/hippunfold/workflow/rules/nnunet.smk b/hippunfold/workflow/rules/nnunet.smk
@@ -133,15 +133,15 @@ rule run_inference:
             suffix="dseg.nii.gz",
             desc="nnunet",
             space="corobl",
-            hemi="{hemi,Lflip|R}"
+            hemi="{hemi}"
         ),
     log:
         bids(
             root="logs",
             **inputs.subj_wildcards,
             suffix="nnunet.txt",
             space="corobl",
-            hemi="{hemi,Lflip|R}"
+            hemi="{hemi}"
         ),
     shadow:
         "minimal"
@@ -171,48 +171,6 @@ rule run_inference:
         "cp {params.temp_lbl} {output.nnunet_seg}"
 
 
-rule unflip_nnunet_nii:
-    """Unflip the Lflip nnunet seg"""
-    input:
-        nnunet_seg=bids(
-            root=work,
-            datatype="anat",
-            **inputs.subj_wildcards,
-            suffix="dseg.nii.gz",
-            desc="nnunet",
-            space="corobl",
-            hemi="{hemi}flip"
-        ),
-        unflip_ref=(
-            bids(
-                root=work,
-                datatype="anat",
-                **inputs.subj_wildcards,
-                suffix="{modality}.nii.gz".format(modality=config["modality"]),
-                space="corobl",
-                desc="preproc",
-                hemi="{hemi}",
-            ),
-        ),
-    output:
-        nnunet_seg=bids(
-            root=work,
-            datatype="anat",
-            **inputs.subj_wildcards,
-            suffix="dseg.nii.gz",
-            desc="nnunet",
-            space="corobl",
-            hemi="{hemi,L}"
-        ),
-    container:
-        config["singularity"]["autotop"]
-    group:
-        "subj"
-    shell:
-        "c3d {input.nnunet_seg} -flip x -popas FLIPPED "
-        " {input.unflip_ref} -push FLIPPED -copy-transform -o {output.nnunet_seg} "
-
-
 def get_f3d_ref(wildcards, input):
     if config["modality"] == "T2w":
         nii = Path(input.template_dir) / config["template_files"][config["template"]][

diff --git a/hippunfold/workflow/rules/preproc_hippb500.smk b/hippunfold/workflow/rules/preproc_hippb500.smk
@@ -35,33 +35,6 @@ rule resample_hippdwi_to_template:
         " -trim 0vox -o {output}"
 
 
-rule lr_flip_b500:
-    input:
-        nii=bids(
-            root=work,
-            datatype="dwi",
-            **inputs.subj_wildcards,
-            suffix="b500.nii.gz",
-            space="corobl",
-            hemi="{hemi}"
-        ),
-    output:
-        nii=bids(
-            root=work,
-            datatype="dwi",
-            **inputs.subj_wildcards,
-            suffix="b500.nii.gz",
-            space="corobl",
-            hemi="{hemi,L}flip"
-        ),
-    container:
-        config["singularity"]["autotop"]
-    group:
-        "subj"
-    shell:
-        "c3d {input} -flip x -o  {output}"
-
-
 rule cp_b500_to_anat_dir:
     input:
         nii=bids(