add back MBMv2 (good for ex vivo marm data)

add missing files

hippunfold/config/snakebids.yml

@@ -160,12 +160,13 @@ 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 MBMv3 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 MBMv2 (ex vivo) or MBMv3 (in vivo) template. (default: %(default)s)'
     default: False
     action: 'store_true'
 
@@ -200,9 +201,10 @@ parse_args:
     choices:
       - 'CITI168'
       - 'dHCP'
+      - 'MBMv2'
       - 'MBMv3'
     default: 'CITI168'
-    help: 'Set the template to use for registration to coronal oblique. (default: %(default)s)'
+    help: 'Set the template to use for registration to coronal oblique (and optionally for template-based segmentation if --use-template-seg is enabled). CITI168 is for adult human data, dHCP is for neonatal human data, MBMv2 is for ex vivo marmoset data, and MBMv3 is for in vivo marmoset data. (default: %(default)s)'
 
   --t1_reg_template:
     help: 'Use T1w to register to template space, instead of the segmentation modality. Note: this was the default behavior prior to v1.0.0.  (default: %(default)s)'
@@ -376,6 +378,15 @@ 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:
+    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 
   MBMv3:
     T1w: resources/tpl-MBMv3/tpl-MBMv3_T1w.nii.gz
     T2w: resources/tpl-MBMv3/tpl-MBMv3_T2w.nii.gz
@@ -416,6 +427,9 @@ 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