Neurolit version bump

README.md

@@ -45,7 +45,7 @@ Modules (all run by default):
 - requires outputs of the `asegdkt` and the `cc` modules as a prerequisite (can be included in the same run).
 
 ### Extensions
-- [FastSurfer-LIT](doc/overview/modules/LIT.md) wraps the FastSurfer segmentation and surface pipelines with lesion inpainting when a lesion mask is provided via `--lesion_mask <path>`. This feature is experimental; review LIT-modified outputs before using them for downstream analyses.
+- [FastSurfer-LIT](doc/overview/modules/LIT.md) wraps the FastSurfer segmentation and surface pipelines with lesion inpainting when a lesion mask is provided via `--lesion_mask <path>`. Review LIT-modified outputs before using them for downstream analyses.
 
 <!-- start of image requirements -->
 ### Requirements to input images

doc/overview/EXAMPLES.md

@@ -246,8 +246,6 @@ When T1w images contain large lesions such as tumors, surgical cavities, or othe
 FastSurfer segmentation and surfaces can be affected by the altered anatomy. FastSurfer can be
 wrapped with the Lesion Inpainting Tool (LIT) by providing `--lesion_mask <path to file>`.
 
-> **Note:** The FastSurfer LIT extension is currently experimental. Review the LIT-modified
-> outputs before using them for downstream analyses.
 
 ### Docker
 ```bash

doc/overview/OUTPUT_FILES.md

@@ -100,9 +100,9 @@ The primary output files are pial, white, and inflated surface files, the thickn
 Lesion Inpainting Tool (LIT, optional)
 --------------------------------------
 When `--lesion_mask <path to file>` is provided, FastSurfer wraps the segmentation and surface
-pipelines with lesion inpainting using LIT. The extension is currently experimental. It inpaints
-the lesion region, runs the requested FastSurfer modules on the inpainted image, and then maps the
-lesion back into the resulting outputs. The current LIT postprocessing workflow updates the primary
+pipelines with lesion inpainting using LIT. It inpaints the lesion region, runs the requested
+FastSurfer modules on the inpainted image, and then maps the lesion back into the resulting outputs.
+The current LIT postprocessing workflow updates the primary
 FastSurfer files in place and keeps the original pre-lesion outputs either as `.lit` backups or,
 for some surface-derived files, in the original `.mapped.*` files.
 

doc/overview/modules/LIT.md

@@ -6,8 +6,6 @@ tool LIT is designed to paint healthy-looking tissue into those lesions, downstr
 FastSurfer can produce more reliable whole-brain segmentation and cortical surface reconstruction
 in cases with significant structural alterations.
 
-> **Note:** The FastSurfer LIT extension is currently experimental. Review the LIT-modified
-> outputs before using them for downstream analyses.
 
 ## FastSurfer Usage
 

doc/scripts/RUN_FASTSURFER.md

@@ -39,7 +39,7 @@ Optional arguments
 * `--no_cereb`: Switch off the cerebellum sub-segmentation.
 * `--no_hypothal`: Skip the hypothalamus segmentation.
 * `--no_cc`: Skip the segmentation and analysis of the corpus callosum.
-* `--lesion_mask <path to file>`: Path to a binary lesion mask in the same space as the T1 input. If provided, FastSurfer will wrap the segmentation and surface pipelines with lesion inpainting using LIT. This experimental feature is useful for images with tumors or other large lesions; review LIT-modified outputs before downstream use.
+* `--lesion_mask <path to file>`: Path to a binary lesion mask in the same space as the T1 input. If provided, FastSurfer will wrap the segmentation and surface pipelines with lesion inpainting using LIT. This feature is useful for images with tumors or other large lesions; review LIT-modified outputs before downstream use.
 * `--cereb_segfile`: Name of the cerebellum segmentation file. If not provided, this intermediate DL-based segmentation will not be stored, but only the merged segmentation will be stored (see --main_segfile <filename>). Requires an ABSOLUTE Path! Default location: \$SUBJECTS_DIR/\$sid/mri/cerebellum.CerebNet.nii.gz
 * `--no_biasfield`: Deactivate the biasfield correction and calculation of partial volume-corrected statistics in the segmentation modules. HypVINN does run but expects that biasfields are corrected externally.
 * `--native_image` or `--keepgeom`: **Only supported for `--seg_only`**. Preserve the native image geometry (orientation, image size, and voxel size) for saved outputs. Internally, FastSurfer may temporarily reorder/flip the image to a soft-LIA layout so the 2D networks still see the expected plane ordering, but written outputs stay in native geometry; only intensity scaling and dtype conversion are applied as needed. This also includes experimental support for anisotropic images (no extreme anisotropy).

pyproject.toml

@@ -68,7 +68,7 @@ qc = [
     'whippersnappy>=2.1',
 ]
 lit = [
-    'neurolit>=0.6.1',
+    'neurolit>=0.7.0',
 ]
 container = [
     'fastsurfer[qc]',

run_fastsurfer.sh

@@ -132,7 +132,7 @@ FLAGS:
   --t1  <T1_input>        T1 full head input (not bias corrected). Requires an
                             ABSOLUTE Path!
   --lesion_mask <mask_input>
-                          Lesion mask input for experimental lesion inpainting.
+                          Lesion mask input for lesion inpainting.
                             Requires an ABSOLUTE Path!
   --asegdkt_segfile <filename>
                           Name of the segmentation file, which includes the
@@ -668,7 +668,7 @@ if [[ -z "$conformed_name" ]] ; then conformed_name="$subject_dir/mri/orig.mgz";
 if [[ -z "$conformed_name_t2" ]] ; then conformed_name_t2="$subject_dir/mri/T2orig.mgz" ; fi
 if [[ -z "$norm_name" ]] ; then norm_name="$subject_dir/mri/orig_nu.mgz" ; fi
 if [[ -z "$norm_name_t2" ]] ; then norm_name_t2="$subject_dir/mri/T2_nu.mgz" ;  fi
-# These files are created by neurolit>=0.6.1 in FastSurfer mode:
+# These files are created by neurolit>=0.7.0 in FastSurfer mode:
 # - lit_inpainting_result: inpainted T1w image from lit-inpainting --fastsurfer_dir.
 # - lit_mask_output: processed lesion mask from lit-inpainting --fastsurfer_dir.
 # - lit_original_mask_output: original input lesion mask copied by lit-inpainting --fastsurfer_dir.