add MBMv3 instead of MBMv2

this template is a group average and better suited for template-based
segmentation of new datasets instead of the ex vivo MBMv2.

Note: hipp segmentation might need some additional tweaks..

hippunfold/config/snakebids.yml

@@ -160,15 +160,20 @@ parse_args:
   --inject_template:
     choices:
       - 'upenn'
-      - 'MBMv2'
+      - 'MBMv3'
     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 marmoset data with the MBMv2 template). (default: %(default)s)'
+    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 marmoset data with the MBMv3 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
+
+
 
   --skip_inject_template_labels:
     help: 'Set this flag to skip post-processing template injection into CNN segmentation. Note this will disable generation of DG surfaces. (default: %(default)s)'
@@ -195,7 +200,7 @@ parse_args:
     choices:
       - 'CITI168'
       - 'dHCP'
-      - 'MBMv2'
+      - 'MBMv3'
     default: 'CITI168'
     help: 'Set the template to use for registration to coronal oblique. (default: %(default)s)'
 
@@ -368,18 +373,18 @@ template_files:
     crop_ref: resources/CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
     crop_refT1w: resources/CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
     Mask_crop: resources/CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
-  MBMv2:
-    T1w: resources/tpl-MBMv2/Template_sym_MTR_80um.nii.gz
-    T2w: resources/tpl-MBMv2/Template_sym_T2_80um.nii.gz
-    xfm_corobl: resources/tpl-MBMv2/tpl-MBMv2_from-native_to-corobl_type-itk_affine.txt
-    crop_ref: resources/tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_T2w.nii.gz
-    crop_refT1w: resources/tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_MTR.nii.gz
-    Mask_crop: resources/tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
-    dseg: resources/tpl-MBMv2/tpl-MBMv2_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
-    coords: resources/tpl-MBMv2/tpl-MBMv2_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
-  upenn:
+    upenn:
     dseg: resources/tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
     coords: resources/tpl-upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
+  MBMv3:
+    T1w: resources/tpl-MBMv3/tpl-MBMv3_T1w.nii.gz
+    T2w: resources/tpl-MBMv3/tpl-MBMv3_T2w.nii.gz
+    xfm_corobl: resources/tpl-MBMv3/tpl-MBMv3_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: resources/tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_T2w.nii.gz
+    crop_refT1w: resources/tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_T1w.nii.gz
+    Mask_crop: resources/tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
+    dseg: resources/tpl-MBMv3/tpl-MBMv3_hemi-R_space-corobl_desc-tissue_dseg.nii.gz
+    coords: resources/tpl-MBMv3/tpl-MBMv3_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
 
 
 
@@ -411,9 +416,9 @@ inject_template_files:
   upenn:
     dseg: resources/tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
     coords: resources/tpl-upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
-  MBMv2:
-    dseg: resources/tpl-MBMv2/tpl-MBMv2_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
-    coords: resources/tpl-MBMv2/tpl-MBMv2_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
+  MBMv3:
+    dseg: resources/tpl-MBMv3/tpl-MBMv3_hemi-R_space-corobl_desc-tissue_dseg.nii.gz
+    coords: resources/tpl-MBMv3/tpl-MBMv3_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
 
 #values to use for re-mapping tissue labels when combining with subfields.
 # set the SRLM and Cyst labels to always be higher than any label in the atlas (so they override)
@@ -594,3 +599,5 @@ generate_myelin_map: False
 no_unfolded_reg: False
 root: results
 use_template_seg: False
+template_seg_smoothing_factor: 2
+

hippunfold/resources/tpl-MBMv3/Snakefile

@@ -0,0 +1,58 @@
+
+configfile: "config.yml"
+
+
+rule all:
+    input:
+        coords=expand(
+            "tpl-{template}_dir-{dir}_hemi-{hemi}_space-corobl_label-{label}_desc-laplace_coords.nii.gz",
+            template=config["template"],
+            dir=["AP", "PD", "IO"],
+            hemi="R",
+            label=["hipp", "dentate"],
+        ),
+
+
+ruleorder: laplace_dentate_AP > laplace_coords
+
+
+rule laplace_coords:
+    input:
+        lbl=lambda wildcards: config["laplace_labels"][wildcards.label][wildcards.dir][
+            "img"
+        ].format(**wildcards),
+    params:
+        gm_labels=lambda wildcards: config["laplace_labels"][wildcards.label][
+            wildcards.dir
+        ]["gm"],
+        src_labels=lambda wildcards: config["laplace_labels"][wildcards.label][
+            wildcards.dir
+        ]["src"],
+        sink_labels=lambda wildcards: config["laplace_labels"][wildcards.label][
+            wildcards.dir
+        ]["sink"],
+        convergence_threshold=1e-5,
+        max_iters=10000,
+    output:
+        coords="tpl-{template}_dir-{dir}_hemi-{hemi}_space-corobl_label-{label}_desc-laplace_coords.nii.gz",
+    log:
+        "logs/tpl-{template}_dir-{dir}_hemi-{hemi}_space-corobl_label-{label}_desc-laplace_coords.txt",
+    script:
+        "../../workflow/scripts/laplace_coords.py"
+
+
+rule laplace_dentate_AP:
+    """ we just mask this from the hipp label"""
+    input:
+        lbl=lambda wildcards: config["laplace_labels"][wildcards.label][wildcards.dir][
+            "img"
+        ].format(**wildcards),
+        coords="tpl-{template}_dir-AP_hemi-{hemi}_space-corobl_label-hipp_desc-laplace_coords.nii.gz",
+    params:
+        gm_labels=lambda wildcards: config["laplace_labels"][wildcards.label][
+            wildcards.dir
+        ]["gm"],
+    output:
+        coords="tpl-{template}_dir-{dir,AP}_hemi-{hemi}_space-corobl_label-{label,dentate}_desc-laplace_coords.nii.gz",
+    shell:
+        "c3d {input.lbl} -retain-labels {params.gm_labels} -binarize {input.coords} -multiply -o {output.coords}"

hippunfold/resources/tpl-MBMv3/config.yml

@@ -0,0 +1,63 @@
+template: MBMv3
+
+laplace_labels:
+  hipp:
+    AP: 
+      img: 'tpl-{template}_hemi-{hemi}_space-corobl_desc-tissue_dseg.nii.gz'
+      gm:
+        - 1
+        - 8
+      src:
+        - 5
+      sink:
+        - 6
+    PD:
+      img: 'tpl-{template}_hemi-{hemi}_space-corobl_desc-tissue_dseg.nii.gz'
+      gm:
+        - 1
+        - 8
+      src:
+        - 3
+      sink:
+        - 8   
+    IO:
+      img: 'tpl-{template}_hemi-{hemi}_space-corobl_desc-tissue_dseg.nii.gz'
+      gm:
+        - 1
+        - 8
+      src:
+        - 2
+        - 4
+        - 7
+      sink:
+        - 0 
+  dentate:
+    AP: 
+      img: 'tpl-{template}_hemi-{hemi}_space-corobl_desc-tissue_dseg.nii.gz'
+      gm:
+        - 8
+      src:
+        - 5
+      sink:
+        - 6
+    PD:
+      img: 'tpl-{template}_hemi-{hemi}_space-corobl_desc-tissueDG_dseg.nii.gz'
+      gm:
+        - 8
+      src:
+        - 1
+      sink:
+        - 2   
+    IO:
+      img: 'tpl-{template}_hemi-{hemi}_space-corobl_desc-tissue_dseg.nii.gz'
+      gm:
+        - 8
+      src:
+        - 1 
+      sink:
+        - 2
+        - 4
+        - 7
+        - 0
+
+

hippunfold/resources/tpl-MBMv3/tpl-MBMv3_from-native_to-corobl_type-itk_affine.txt

@@ -0,0 +1,5 @@
+#Insight Transform File V1.0
+#Transform 0
+Transform: MatrixOffsetTransformBase_double_3_3
+Parameters: 0.967355 -0.004634807426139079 -0.000258298981039498 -0.00140371 0.517115683952737 -0.8054876155601979 -0.0102109 0.7566899552250975 0.5498342828466409 0.06143197478192646 -8.855894869646765 5.349429146692667
+FixedParameters: 0 0 0

hippunfold/workflow/rules/templateseg.smk

@@ -1,9 +1,20 @@
+def get_smoothing_opt(wildcards):
+    """sets the smoothness of the greedy template shape injection deformation"""
+
+    gradient_sigma = 1.732 * float(config["template_seg_smoothing_factor"])
+    warp_sigma = 0.7071 * float(config["template_seg_smoothing_factor"])
+
+    return f"-s {gradient_sigma}vox {warp_sigma}vox"
+
+
 rule template_reg:
     input:
         moving_img=lambda wildcards: os.path.join(
             workflow.basedir,
             "..",
-            config["template_files"][config["template"]][config["modality"]],
+            config["template_files"][config["template"]][
+                get_modality_suffix(config["modality"])
+            ],
         ),
         xfm_corobl=lambda wildcards: os.path.join(
             workflow.basedir,
@@ -14,14 +25,18 @@ rule template_reg:
             root=work,
             datatype="anat",
             **config["subj_wildcards"],
-            suffix=f"{config['modality']}.nii.gz",
+            suffix="{modality}.nii.gz".format(
+                modality=get_modality_suffix(config["modality"])
+            ),
             space="corobl",
             desc="preproc",
-            hemi="{hemi}",
+            hemi="{hemi}"
         ),
     params:
         general_opts="-d 3 -m NCC 2x2x2",
-        greedy_opts="-n 100x50x10 -s 4vox 2vox",  #default is 1.732vox, 0.7071vox
+        smoothing_opts=get_smoothing_opt,
+        iteration_opts="-n 100x50x10",  #default -n 100x100
+        img_pairs=lambda wildcards, input: "-i {input.fixed_img} {input.moving_img}",
     output:
         warp=bids(
             root=work,
@@ -40,8 +55,9 @@ rule template_reg:
         config["singularity"]["autotop"]
     threads: 8
     shell:
-        "greedy -threads {threads} {params.general_opts} {params.greedy_opts} "
-        " -i {input.fixed_img} {input.moving_img} -it {input.xfm_corobl} -o {output.warp}"
+        "greedy -threads {threads} {params.general_opts} "
+        " {params.smoothing_opts} {params.iteration_opts} "
+        " {params.img_pairs} -it {input.xfm_corobl} -o {output.warp}"
 
 
 rule warp_template_dseg: