changes work macaque local test

khanlab · Feb 21, 2024 · e1b674c · e1b674c
1 parent 29647cf
commit e1b674c
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Showing 6 changed files with 99 additions and 21 deletions.
diff --git a/.dryrun_test_all.sh b/.dryrun_test_all.sh
@@ -14,3 +14,4 @@ hippunfold - test_out participant -np --modality cropseg --path_cropseg test_dat
 hippunfold - test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L
 hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template
 hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w
+hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg
diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
@@ -366,6 +366,29 @@ singularity:
 
 xfm_identity: resources/etc/identity_xfm.txt
 
+#templates enabled for template-based segmentation are here
+template_based_segmentation:
+  CITI168:
+    hemi:
+      - R
+      - L
+  dHCP:
+    hemi:
+      - R
+      - L
+  CIVM:
+    hemi:
+      - R
+      - L
+  MBMv2:
+    hemi:
+      - R
+      - L
+  MBMv3:
+    hemi:
+      - R
+
+
 template_files:
   CITI168:
     T1w: T1w_head_700um.nii.gz
@@ -395,16 +418,16 @@ template_files:
     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
+    crop_ref: tpl-MBMv3_hemi-{hemi}_space-corobl_T1w.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
+    dseg: tpl-MBMv3_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz
+    coords: tpl-MBMv3_dir-{dir}_hemi-{hemi}_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
+    dseg: tpl-CIVM_hemi-R_space-corobl_desc-tissuemanual_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
@@ -491,6 +514,7 @@ resource_urls:
     MBMv2: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0887852d133ca597dd/?zip='
     MBMv3: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0e8a28b11240ffc6e9/?zip='
     upenn: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c1613d27b122a94ca09/?zip='
+    CIVM: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bf62827451220b86e24/?zip='
 #to get hash, see https://github.com/CenterForOpenScience/osf.io/issues/8256#issuecomment-379833911
 
 

diff --git a/hippunfold/workflow/rules/download.smk b/hippunfold/workflow/rules/download.smk
@@ -3,14 +3,32 @@
 download_dir = get_download_dir()
 
 
-rule download_extract_atlas_or_template:
+rule download_extract_atlas:
     params:
-        url=lambda wildcards: config["resource_urls"][wildcards.resource_type][
+        url=lambda wildcards: config["resource_urls"]["atlas"][
             wildcards.atlas
         ],
     output:
         unzip_dir=directory(
-            Path(download_dir) / "{resource_type,atlas|template}" / "{atlas}"
+            Path(download_dir) / "atlas" / "{atlas}"
+        ),
+    container:
+        config["singularity"]["autotop"]
+    shadow:
+        "minimal"
+    shell:
+        "wget https://{params.url} -O temp.zip && "
+        " unzip -d {output.unzip_dir} temp.zip"
+
+
+rule download_extract_template:
+    params:
+        url=lambda wildcards: config["resource_urls"]["template"][
+            wildcards.template
+        ],
+    output:
+        unzip_dir=directory(
+            Path(download_dir) / "template" / "{template}"
         ),
     container:
         config["singularity"]["autotop"]

diff --git a/hippunfold/workflow/rules/preproc_t1.smk b/hippunfold/workflow/rules/preproc_t1.smk
@@ -298,7 +298,7 @@ rule warp_t1_to_corobl_crop:
             root=work,
             datatype="anat",
             **config["subj_wildcards"],
-            suffix="T1w.nii.gz",
+            suffix="{modality}.nii.gz",
             space="corobl",
             desc="preproc",
             hemi="{hemi,L|R}"

diff --git a/hippunfold/workflow/rules/templateseg.smk b/hippunfold/workflow/rules/templateseg.smk
@@ -7,6 +7,39 @@ def get_smoothing_opt(wildcards):
     return f"-s {gradient_sigma}vox {warp_sigma}vox"
 
 
+# Template-based segmentation supports templates that have only a single hemisphere
+# by mapping it to the flipped version of the other hemisphere.
+# If a template has both L and R files, then we set hemi_constrained_wildcard to L|R.
+# If a hemisphere is missing data, then we set it to flip that, e.g. if L missing, then use Lflip|R
+
+hemi_constraints = []
+if config["template"] in config["template_based_segmentation"]:
+    for hemi in config["hemi"]:
+        if hemi in config["template_based_segmentation"][config["template"]]["hemi"]:
+            hemi_constraints.append(hemi)
+        else:
+            hemi_constraints.append(f"{hemi}flip")
+
+hemi_constrained_wildcard = "{{hemi,{constraints}}}".format(
+    constraints="|".join(hemi_constraints)
+)
+
+
+def flipped(wildcards):
+    """function to map hemi in wildcards from Lflip to R, or Rflip to L,
+    for use in rules where e.g. the output wildcard is Lflip, but for the input, R is desired, such as
+    when mapping a R hemi dseg to the Lflip hemisphere of a subject."""
+
+    if wildcards.hemi == "L" or wildcards.hemi == "R":
+        return wildcards
+    elif wildcards.hemi == "Lflip":
+        wildcards.hemi = "R"
+        return wildcards
+    elif wildcards.hemi == "Rflip":
+        wildcards.hemi = "L"
+        return wildcards
+
+
 rule template_reg:
     input:
         fixed_img=bids(
@@ -25,7 +58,7 @@ rule template_reg:
         moving_img=lambda wildcards, input: Path(input.template_dir)
         / config["template_files"][config["template"]][
             get_modality_suffix(config["modality"])
-        ].format(**wildcards),
+        ].format(**flipped(wildcards)),
         xfm_corobl=lambda wildcards, input: Path(input.template_dir)
         / config["template_files"][config["template"]]["xfm_corobl"].format(
             **wildcards
@@ -43,7 +76,7 @@ rule template_reg:
             from_="template",
             to="subject",
             space="corobl",
-            hemi="{hemi,R|L}"
+            hemi=hemi_constrained_wildcard,
         ),
     group:
         "subj"
@@ -81,7 +114,9 @@ rule warp_template_dseg:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         template_dseg=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["dseg"].format(**wildcards),
+        / config["template_files"][config["template"]]["dseg"].format(
+            **flipped(wildcards)
+        ),
         interp_opt="-ri LABEL 0.2vox",
     output:
         inject_seg=bids(
@@ -91,7 +126,7 @@ rule warp_template_dseg:
             suffix="dseg.nii.gz",
             desc="postproc",
             space="corobl",
-            hemi="{hemi,R|L}"
+            hemi=hemi_constrained_wildcard,
         ),
     group:
         "subj"
@@ -128,7 +163,9 @@ rule warp_template_coords:
     params:
         interp_opt="-ri NN",
         template_coords=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["coords"].format(**wildcards),
+        / config["template_files"][config["template"]]["coords"].format(
+            **flipped(wildcards)
+        ),
     output:
         init_coords=bids(
             root=work,
@@ -139,7 +176,7 @@ rule warp_template_coords:
             suffix="coords.nii.gz",
             desc="init",
             space="corobl",
-            hemi="{hemi,R|L|Lflip}"
+            hemi=hemi_constrained_wildcard,
         ),
     group:
         "subj"
@@ -176,7 +213,7 @@ rule warp_template_anat:
     params:
         template_anat=lambda wildcards, input: Path(input.template_dir)
         / config["template_files"][config["template"]][config["modality"]].format(
-            **wildcards
+            **flipped(wildcards)
         ),
         xfm_corobl=lambda wildcards, input: Path(input.template_dir)
         / config["template_files"][config["template"]]["xfm_corobl"].format(
@@ -190,7 +227,7 @@ rule warp_template_anat:
             suffix=f"{config['modality']}.nii.gz",
             desc="warpedtemplate",
             space="corobl",
-            hemi="{hemi,L|R}",
+            hemi=hemi_constrained_wildcard,
         ),
     group:
         "subj"
@@ -228,7 +265,7 @@ rule unflip_template_dseg:
             suffix="dseg.nii.gz",
             desc="postproc",
             space="corobl",
-            hemi="{hemi,L}",
+            hemi="{hemi,L|R}",
             **config["subj_wildcards"]
         ),
     container:
@@ -272,7 +309,7 @@ rule unflip_template_coords:
             suffix="coords.nii.gz",
             desc="init",
             space="corobl",
-            hemi="{hemi,L}"
+            hemi="{hemi,L|R}",
         ),
     container:
         config["singularity"]["autotop"]

diff --git a/hippunfold/workflow/scripts/create_warps.py b/hippunfold/workflow/scripts/create_warps.py
@@ -259,9 +259,7 @@ def summary(name, array):
 summary("displace_to_unfold_vec", displace_to_unfold_vec)
 
 # create new shape as 5d vector image in native space
-native_map_shape = np.ones(
-    5,
-)
+native_map_shape = np.ones(5,)
 native_map_shape[:3] = mask.shape
 native_map_shape[-1] = 3