use downloaded template for shape-inject

khanlab · Feb 16, 2024 · d3ccc76 · d3ccc76
1 parent d73576e
commit d3ccc76
Show file tree

Hide file tree

Showing 3 changed files with 34 additions and 39 deletions.
diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
@@ -382,32 +382,32 @@ template_files:
     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: MBMv2/Template_sym_MTR_80um.nii.gz
-    T2w: MBMv2/Template_sym_T2_80um.nii.gz
-    xfm_corobl: MBMv2/tpl-MBMv2_from-native_to-corobl_type-itk_affine.txt
-    crop_ref: MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_{modality}.nii.gz
-    Mask_crop: MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
-    dseg: MBMv2/tpl-MBMv2_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
-    coords: MBMv2/tpl-MBMv2_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+    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: MBMv3/tpl-MBMv3_T1w.nii.gz
-    T2w: MBMv3/tpl-MBMv3_T2w.nii.gz
-    xfm_corobl: MBMv3/tpl-MBMv3_from-native_to-corobl_type-itk_affine.txt
-    crop_ref: MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_{modality}.nii.gz
-    Mask_crop: MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
-    dseg: MBMv3/tpl-MBMv3_hemi-R_space-corobl_desc-tissue_dseg.nii.gz
-    coords: MBMv3/tpl-MBMv3_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+    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: CIVM/tpl-CIVM_T1w.nii.gz
-    xfm_corobl: CIVM/tpl-CIVM_from-native_to-corobl_type-itk_affine.txt
-    crop_ref: CIVM/tpl-CIVM_hemi-{hemi}_space-corobl_{modality}.nii.gz
-    Mask_crop: CIVM/tpl-CIVM_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
-    dseg: CIVM/tpl-CIVM_hemi-R_space-corobl_desc-tissue_dseg.nii.gz
-    coords: CIVM/tpl-CIVM_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+    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: upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
-    dseg: upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
-    coords: upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
+    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:
@@ -458,6 +458,8 @@ no_reg_template: False
 
 modality: T2w
 
+inject_template: upenn
+
 template: CITI168
 
 atlas: 

diff --git a/hippunfold/workflow/rules/preproc_t1.smk b/hippunfold/workflow/rules/preproc_t1.smk
@@ -245,7 +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"

diff --git a/hippunfold/workflow/rules/shape_inject.smk b/hippunfold/workflow/rules/shape_inject.smk
@@ -88,13 +88,10 @@ rule prep_segs_for_greedy:
 
 rule import_template_shape:
     input:
-        template_seg=os.path.join(
-            workflow.basedir,
-            "..",
-            "resources",
-            "tpl-upenn",
-            "tpl-upenn_desc-hipptissue_dseg.nii.gz",
-        ),
+        template_dir=Path(download_dir) / "template" / config["inject_template"],
+    params:
+        template_seg=lambda wildcards, input: Path(input.template_dir)
+        / config["template_files"][config["inject_template"]]["dseg"],
     output:
         template_seg=bids(
             root=work,
@@ -279,13 +276,6 @@ rule template_shape_inject:
 
 rule inject_init_laplace_coords:
     input:
-        coords=os.path.join(
-            workflow.basedir,
-            "..",
-            "resources",
-            "tpl-upenn",
-            "tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz",
-        ),
         subject_seg=get_input_for_shape_inject,
         matrix=bids(
             root=work,
@@ -310,7 +300,10 @@ rule inject_init_laplace_coords:
             space="corobl",
             hemi="{hemi}"
         ),
+        template_dir=Path(download_dir) / "template" / config["inject_template"],
     params:
+        coords=lambda wildcards, input: Path(input.template_dir)
+        / config["template_files"][config["inject_template"]]["coords"],
         interp_opt="-ri NN",
     output:
         init_coords=bids(
@@ -340,7 +333,7 @@ rule inject_init_laplace_coords:
         config["singularity"]["autotop"]
     threads: 8
     shell:
-        "greedy -d 3 -threads {threads} {params.interp_opt} -rf {input.subject_seg} -rm {input.coords} {output.init_coords}  -r {input.warp} {input.matrix} &> {log}"
+        "greedy -d 3 -threads {threads} {params.interp_opt} -rf {input.subject_seg} -rm {params.coords} {output.init_coords}  -r {input.warp} {input.matrix} &> {log}"
 
 
 rule unflip_init_coords: