Docs: surgical updates for merged best-practice batch

Bring the prose docs in line with the 9 PRs merged on main:
- Brainstem subdivision: Talairach removed -> FreeSurfer substructures
  (Iglesias 2015 segmentBS: midbrain/pons/medulla/SCP) via
  BRAINSTEM_SEGMENTATION_METHOD; Harvard-Oxford now gross-extent only
  (maxprob-thr25).
- Brain extraction: BET/ANTs -> SynthStrip primary with
  SynthStrip -> ANTs(Otsu) -> BET fallback, robustfov neck removal,
  posterior-fossa QC gate (BRAIN_EXTRACTION_METHOD).
- Denoising: Rician-only -> modality-aware dispatcher (NLM for
  T1/T2/FLAIR, MP-PCA dwidenoise for DWI, SWI/TOF skipped) + DWI path.
- N4: field strength tunes b-spline (-b); gentler lesion-aware FLAIR.
- Registration: MI for cross-modality SyN, winsorization, label-aware
  GenericLabel interpolation.
- Detection: CSF/PV exclusion via FAST CSF PVE; single authoritative
  fallback SD multiplier (THRESHOLD_WM_SD_MULTIPLIER).
- New optional supervised WMH modules: FSL BIANCA, LST-AI + SAMSEG.

Files: README.md, docs/README.md, docs/TECHNICAL_OVERVIEW.md,
docs/README_tests.md. Also tracks the two previously-untracked design
docs: brainstem_freesurfer_segmentation_spec.md (now IMPLEMENTED banner,
#119) and complete_pipeline_analysis_and_fix_plan.md (DONE markers on
addressed items).

Multi-atlas docs and CLAUDE.md are intentionally out of scope (handled
separately).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Author: davidj-brewster

README.md

@@ -55,7 +55,7 @@ source ~/.bash_profile && src/pipeline.sh -i ../DiCOM -o ../mri_results -s patie
 The pipeline consists of 8 resumable stages:
 
 1. **import** - DICOM import and conversion
-2. **preprocess** - Rician denoising + N4 bias correction
+2. **preprocess** - Modality-aware denoising (Rician NLM for T1/T2/FLAIR, MP-PCA for DWI) + N4 bias correction
 3. **brain_extraction** - Brain extraction and standardization
 4. **registration** - Multi-stage alignment to standard space
 5. **segmentation** - Brainstem and pons region extraction
@@ -81,8 +81,8 @@ Active development as of June 2026. While functional, improvements are ongoing.
 This pipeline leverages established neuroimaging tools:
 - **ANTs** - Advanced Normalizations Tools
 - **FSL** - FMRIB Software Library
-- **FreeSurfer** - 3D visualization
-- **Harvard-Oxford & Talairach Atlases** - Brainstem segmentation
+- **FreeSurfer** - Brainstem substructure segmentation (Iglesias 2015 `segmentBS`) + 3D visualization
+- **Harvard-Oxford Atlas** - Gross brainstem extent mask
 - **MNI152 Templates** - Registration targets
 
 ## License