cropseg to manualseg

.github/workflows/python-testing.yml

@@ -94,13 +94,13 @@ jobs:
         run: |
           poetry run hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w
 
-      - name: Test cropseg bids, with path override
+      - name: Test manualseg bids, with path override
         run: |
-          poetry run hippunfold test_data/data_cropseg test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
+          poetry run hippunfold test_data/bids_manualseg test_out participant -np --modality manualseg --path_manualseg test_data/bids_manualseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
 
-      - name: Test cropseg bids, one hemisphere hemi
+      - name: Test manualseg bids, one hemisphere hemi
         run: |
-          poetry run hippunfold test_data/data_cropseg_1hemi test_out participant -np --modality cropseg --hemi L
+          poetry run hippunfold test_data/bids_manualseg_1hemi test_out participant -np --modality manualseg --hemi L
 
       - name: Test T2w with T1w template registration
         run: |

hippunfold/config/snakebids.yml

@@ -67,7 +67,7 @@ pybids_inputs:
       - acquisition
       - run
 
-  cropseg:
+  manualseg:
     filters:
       suffix: 'dseg'
       extension: '.nii.gz'
@@ -88,13 +88,13 @@ pybids_inputs:
 parse_args:
 
   --modality:
-    help: 'Type of image to run hippunfold on. For manual segmentations, use cropseg and be sure to match the label scheme applied in the look up table (lut) online. For best performance, please also make sure the input is approximately aligned to the template space, with hemi-L|R in the name. (default: %(default)s)'
+    help: 'Type of image to run hippunfold on. For manualseg and be sure to match the label scheme applied in the look up table (lut) online. For best performance, please also make sure the input is approximately aligned to the template space, with separate hemi-L|R in the name(s). (default: %(default)s)'
     required: True
     choices:
       - T1w
       - T2w
       - hippb500
-      - cropseg
+      - manualseg
 
 
   --template:

hippunfold/workflow/Snakefile

@@ -35,7 +35,7 @@ if (
     limit_to_list.add("T2w")
 if (
     config["modality"] == "hippb500"
-    or config["modality"] == "cropseg"
+    or config["modality"] == "manualseg"
     or "corobl" in config["output_spaces"]
 ):
     ref_spaces.append("corobl")
@@ -111,9 +111,9 @@ if "T1w" in limit_to_list:
 
 
 # include rules only as they are needed..
-if config["modality"] == "cropseg":
+if config["modality"] == "manualseg":
 
-    include: "rules/preproc_cropseg.smk"
+    include: "rules/preproc_manualseg.smk"
 
 else:
 

hippunfold/workflow/rules/preproc_cropseg.smk → hippunfold/workflow/rules/preproc_manualseg.smk

@@ -1,7 +1,7 @@
 
-rule import_cropseg_to_corobl:
+rule import_manualseg_to_corobl:
     input:
-        in_img=partial(get_single_bids_input, component="cropseg"),
+        in_img=partial(get_single_bids_input, component="manualseg"),
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         std_to_cor=lambda wildcards: config["template_files"][config["template"]][

hippunfold/workflow/rules/qc.smk

@@ -120,7 +120,7 @@ def get_bg_img_for_subfield_qc(wildcards):
             hemi="{hemi}",
             **inputs.subj_wildcards,
         )
-    elif config["modality"] == "cropseg":
+    elif config["modality"] == "manualseg":
         # blank image as bg
         return bids(
             root=work,

hippunfold/workflow/rules/shape_inject.smk

@@ -32,7 +32,7 @@ def flipped(wildcards):
 
 
 def get_input_for_shape_inject(wildcards):
-    if config["modality"] == "cropseg":
+    if config["modality"] == "manualseg":
         seg = bids(
             root=work,
             datatype="anat",
@@ -55,7 +55,7 @@ def get_input_for_shape_inject(wildcards):
 
 
 def get_input_splitseg_for_shape_inject(wildcards):
-    if config["modality"] == "cropseg":
+    if config["modality"] == "manualseg":
         seg = bids(
             root=work,
             datatype="anat",