patch-templateseg-dHCP (#307)

* patch-templateseg-dHCP

Missed this in #304 (caught in wet-run)

* minor bugs caught in wet-run testing

hippunfold/config/snakebids.yml

@@ -414,23 +414,24 @@ template_files:
     crop_ref: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_T2w.nii.gz
     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
+    dseg: tpl-dHCP_space-corobl_hemi-{hemi}_desc-tissuemanualseg_dseg.nii.gz
     coords: tpl-dHCP_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
   MBMv2:
     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
+    crop_ref: tpl-MBMv2_hemi-R_space-corobl_{modality}.nii.gz
+    Mask_crop: tpl-MBMv2_hemi-R_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: 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_T1w.nii.gz
-    Mask_crop: tpl-MBMv3_hemi-{hemi}_space-corobl_desc-hipp_mask.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
+    crop_ref: tpl-MBMv3_hemi-R_space-corobl_T1w.nii.gz
+    Mask_crop: tpl-MBMv3_hemi-R_space-corobl_desc-hipp_mask.nii.gz
+    dseg: tpl-MBMv3_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
+    coords: tpl-MBMv3_dir-{dir}_hemi-R_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
@@ -468,7 +469,7 @@ atlas_files:
     label_list: magdeburg_labellist.txt
   freesurfer:
     label_nii: sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz
-    lut: desc-subfields_atlas-mfreesurfer_dseg.tsv
+    lut: desc-subfields_atlas-freesurfer_dseg.tsv
     label_list: freesurfer_labellist.txt
   macaque:
     label_nii: sub-bigmac_hemi-{hemi}_space-unfold_label-hipp_desc-macaquesubfields_dseg.nii.gz
@@ -507,7 +508,10 @@ tissue_atlas_mapping:
     dg: 6
     srlm: 7
     cyst: 8
-
+  macaque: 
+    dg: 6
+    srlm: 7
+    cyst: 8
 
 rigid_reg_template: False
 no_reg_template: False