Fix output file documentation

Add hypvinn url file

HypVINN/config/checkpoint_paths.yaml

@@ -0,0 +1,7 @@
+url:
+- "https://b2share.fz-juelich.de/api/files/7133b542-733b-4cc6-a284-5c333ff25f78"
+
+checkpoint:
+  axial: "checkpoints/HypVINN_axial_v1.0.0.pkl"
+  coronal: "checkpoints/HypVINN_coronal_v1.0.0.pkl"
+  sagittal: "checkpoints/HypVINN_sagittal_v1.0.0.pkl"

HypVINN/utils/checkpoint.py

@@ -12,24 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-# IMPORTS
-import os
-
-from FastSurferCNN.utils import logging
-from FastSurferCNN.utils.checkpoint import (
-    FASTSURFER_ROOT,
-    load_from_checkpoint,
-    create_checkpoint_dir,
-    get_checkpoint,
-    get_checkpoint_path,
-    save_checkpoint,
-)
-
-logger = logging.get_logger(__name__)
-
-# Defaults
-URL = "https://b2share.fz-juelich.de/api/files/7133b542-733b-4cc6-a284-5c333ff25f78"
-HYPVINN_AXI = os.path.join(FASTSURFER_ROOT, "checkpoints/HypVINN_axial_v1.0.0.pkl")
-HYPVINN_COR = os.path.join(FASTSURFER_ROOT, "checkpoints/HypVINN_coronal_v1.0.0.pkl")
-HYPVINN_SAG = os.path.join(FASTSURFER_ROOT, "checkpoints/HypVINN_sagittal_v1.0.0.pkl")
+from FastSurferCNN.utils.parser_defaults import FASTSURFER_ROOT
 
+YAML_DEFAULT = FASTSURFER_ROOT / "CerebNet/config/checkpoint_paths.yaml"

doc/overview/OUTPUT_FILES.md

@@ -25,6 +25,24 @@ The cerebellum module outputs the files in the table shown below. Unless switche
 | mri         | cerebellum.CerebNet.nii.gz    | cerebnet  | cerebellum sub-segmentation|
 | stats       | cerebellum.CerebNet.stats     | cerebnet  | table of cerebellum segmentation statistics|
 
+## HypVINN module
+
+The hypothalamus module outputs the files in the table shown below. Unless switched off by the `--no_hypvinn` argument, this module is automatically run whenever the segmentation module is run. It adds three files, an image with the sub-segmentation of the hypothalamus and a text file with summary statistics.
+
+
+| directory   | filename                         | module  | description                                   |
+|:------------|----------------------------------|---------|-----------------------------------------------|
+| mri         | hypothalamus.HypVINN.nii.gz      | hypvinn | hypothalamus sub-segmentation                 |
+| mri         | hypothalamus_mask.HypVINN.nii.gz | hypvinn | hypothalamus sub-segmentation mask            |
+| stats       | hypothalamus.HypVINN.stats       | hypvinn | table of hypothalamus segmentation statistics |
+
+If a T2 image is also passed, the following images are created.
+
+| directory | filename        | module  | description                    |
+|:----------|-----------------|---------|--------------------------------|
+| mri       | T2_orig.mgz     | hypvinn | conformed T2 image             |
+| mri       | T2_orig_nu.mgz  | hypvinn | biasfield-corrected T2 image   |
+| mri       | T2_nu_reg.mgz   | hypvinn | co-registered T2 to orig image |
 
 ## Surface module