added use_template_seg option, and MBMv2 files

still a WIP

TODO: clean-up config and CLI for specifying templates -- right now
--template and --template_files is used to select the rigid/affine reg template, and
--inject_template and --inject_files is used to select the template shape injection or
registration-based segmentation template (for use_template_seg).. could
harmonize the structure for files, and keep separate flags..

hippunfold/config/snakebids.yml

@@ -164,6 +164,11 @@ parse_args:
     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. 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)'
+    default: False
+    action: 'store_true'
+
 
   --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)'
@@ -580,3 +585,4 @@ t1_reg_template: False
 generate_myelin_map: False
 no_unfolded_reg: False
 root: results
+use_template_seg: False

hippunfold/resources/tpl-MBMv2/Snakefile

@@ -0,0 +1,38 @@
+
+configfile: 'config.yml'
+
+rule all: 
+    input:
+        coords=expand('tpl-{template}_dir-{dir}_hemi-{hemi}_space-corobl_label-{label}_desc-laplace_coords.nii.gz',
+                template='MBMv2',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-MBMv2/config.yml

@@ -0,0 +1,61 @@
+laplace_labels:
+  hipp:
+    AP: 
+      img: 'tpl-{template}_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz'
+      gm:
+        - 1
+        - 8
+      src:
+        - 5
+      sink:
+        - 6
+    PD:
+      img: 'tpl-{template}_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz'
+      gm:
+        - 1
+        - 8
+      src:
+        - 3
+      sink:
+        - 8   
+    IO:
+      img: 'tpl-{template}_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz'
+      gm:
+        - 1
+        - 8
+      src:
+        - 2
+        - 4
+        - 7
+      sink:
+        - 0 
+  dentate:
+    AP: 
+      img: 'tpl-{template}_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz'
+      gm:
+        - 8
+      src:
+        - 5
+      sink:
+        - 6
+    PD:
+      img: 'tpl-{template}_hemi-{hemi}_space-corobl_desc-tissueDGmanual_dseg.nii.gz'
+      gm:
+        - 8
+      src:
+        - 1
+      sink:
+        - 2   
+    IO:
+      img: 'tpl-{template}_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz'
+      gm:
+        - 8
+      src:
+        - 1 
+      sink:
+        - 2
+        - 4
+        - 7
+        - 0
+
+

hippunfold/resources/tpl-MBMv2/tpl-MBMv2_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: 1 0 0 0 0.6018150231520484 -0.7986355100472928 0 0.7986355100472928 0.6018150231520484 0 2.2613285618049965 -4.855523654670475
+FixedParameters: 0 0 0

hippunfold/workflow/Snakefile

@@ -143,7 +143,6 @@ include: "rules/autotop.smk"
 include: "rules/warps.smk"
 
 
-include: "rules/shape_inject.smk"
 
 
 include: "rules/gifti.smk"
@@ -160,7 +159,10 @@ include: "rules/qc.smk"
 
 include: "rules/myelin_map.smk"
 
-include: "rules/templateseg.smk"
+if config['use_template_seg']:
+    include: "rules/templateseg.smk"
+else:
+    include: "rules/shape_inject.smk"
 
 rule all:
     input:

hippunfold/workflow/rules/common.smk

@@ -292,7 +292,7 @@ def get_final_qc():
                 allow_missing=True,
             )
         )
-    if (config["modality"] == "T1w") or (config["modality"] == "T2w"):
+    if (config["modality"] == "T1w") or (config["modality"] == "T2w") and not config['use_template_seg']:
         qc.extend(
             expand(
                 bids(