minor bugfix for passing modality

khanlab · Dec 16, 2024 · d128ba8 · d128ba8
1 parent 329e213
commit d128ba8
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/.dryrun_test_all.sh b/.dryrun_test_all.sh
@@ -9,9 +9,8 @@ hippunfold test_data/bids_T1w test_out participant -np --modality T1w
 hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500 
 hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w 
 hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w 
-hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w 
-hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz 
-hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L 
+hippunfold test_data/bids_manualseg test_out participant -np --modality manualseg --path_manualseg test_data/bids_manualseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
+hippunfold test_data/bids_manualseg_1hemi test_out participant -np --modality manualseg --hemi L
 hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template 
 hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w 
 hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg 
diff --git a/hippunfold/workflow/Snakefile b/hippunfold/workflow/Snakefile
@@ -20,14 +20,13 @@ template_modality = False
 # set the lists used for output spaces
 if (
     config["modality"] == "T1w"
-    or config["modality"] == "segT1w"
     or "T1w" in config["output_spaces"]
 ):
     ref_spaces.append("T1w")
     crop_ref_spaces.append("cropT1w")
     limit_to_list.add("T1w")
 if (
-    (config["modality"] == "T2w" or config["modality"] == "segT2w")
+    config["modality"] == "T2w"
     and "native" in config["output_spaces"]
 ) or "T2w" in config["output_spaces"]:
     ref_spaces.append("T2w")
@@ -64,6 +63,7 @@ elif "T1w" in config["modality"]:
 if config["skip_inject_template_labels"]:  # TODO do we need this?
     config["autotop_labels"] = ["hipp"]
 
+limit_to_list.add(config["modality"])
 
 # if atlas doesn't contain alignment features
 if not config["atlas"] == ["multihist7"]: