Add some more context

Author: nx10

src/rbc/anatomical/__init__.py

@@ -1,8 +1,11 @@
 """Anatomical preprocessing.
 
-This module defines anatomical MRI preprocessing steps for RBC datasets,
-including:
+This module defines anatomical MRI preprocessing steps for RBC pipeline.
 
-- Initial anatomical preprocessing
-- Tissue segmentation using FSL FAST
+Anatomical preprocessing prepares T1-weighted structural brain images for
+analysis. The T1 provides high-resolution anatomy used to align functional
+data and identify tissue types (gray matter, white matter, CSF).
+
+Steps: reorientation, skull stripping (ANTs), N4 bias correction, tissue
+segmentation (FSL FAST), and registration to MNI152 template.
 """

src/rbc/cli/__init__.py

@@ -1,4 +1,7 @@
 """Command line interface.
 
-This module handles CLI entry points.
+This module handles CLI entry points for the RBC pipeline.
+
+Parses arguments, validates BIDS inputs, and dispatches to workflow modules.
+Subcommands are defined in rbc.cli.* modules.
 """

src/rbc/cli/anatomical.py

@@ -1,4 +1,5 @@
-"""Anatomical preprocessing.
+"""Anatomical preprocessing CLI.
 
-This module handles CLI for anatomical preprocessing workflows.
+Command-line interface for anatomical preprocessing workflows.
+Calls into rbc.workflows.anatomical.
 """

src/rbc/cli/derivatives.py

@@ -1,4 +1,5 @@
-"""Derivative computations.
+"""Derivative computations CLI.
 
-This module handles CLI for derivative computations.
+Command-line interface for computing derivatives (ALFF/fALFF, ReHo, network
+centrality, atlas-based timeseries) from preprocessed data.
 """

src/rbc/cli/functional.py

@@ -1,4 +1,5 @@
-"""Functional preprocessing.
+"""Functional preprocessing CLI.
 
-This module handles CLI for functional preprocessing workflows.
+Command-line interface for functional preprocessing workflows.
+Requires anatomical preprocessing to have been run first.
 """

src/rbc/cli/longitudinal.py

@@ -1,4 +1,5 @@
 """Longitudinal CLI.
 
-This module handles the longitudinal CLI.
+Command-line interface for longitudinal workflows. Creates within-subject
+templates and processes multiple sessions.
 """

src/rbc/cli/qc.py

@@ -1,4 +1,5 @@
 """Quality control CLI.
 
-This module handles CLI for QC metrics.
+Command-line interface for computing QC metrics. Outputs reports with
+pass/fail flags based on RBC thresholds.
 """

src/rbc/functional/__init__.py

@@ -1,13 +1,13 @@
 """Functional preprocessing.
 
-This module defines functional MRI preprocessing steps for RBC datasets,
-including:
+This module defines functional MRI preprocessing steps for RBC datasets.
 
-- Functional initialization
-- Motion correction
-- Slice timing correction
-- Despiking
-- BOLD brain masking
-- Boundary-based registration (BBR) coregistration
-- Single-step resampling to template space
+Functional MRI measures brain activity over time via the BOLD signal. Raw
+fMRI contains motion artifacts, timing differences, and distortions that
+must be corrected before analysis.
+
+Steps: reorientation, TR truncation, motion correction (mcflirt), slice
+timing correction (3dTshift), despiking (3dDespike), brain masking,
+coregistration to T1w (FLIRT BBR), and single-step resampling to 2mm MNI
+space.
 """

src/rbc/longitudinal/__init__.py

@@ -1,4 +1,8 @@
 """Longitudinal workflow.
 
-This module handles the longitudinal workflow.
+This module handles longitudinal preprocessing for multi-session data.
+
+Creates an unbiased within-subject anatomical template and processes each
+session relative to it, improving sensitivity for detecting changes over
+time in developmental studies.
 """

src/rbc/qc/__init__.py

@@ -1,11 +1,8 @@
 """Quality control.
 
-This module defines quality control metrics for RBC datasets,
-including:
+This module defines quality control metrics for RBC datasets.
 
-- XCP-style quality control outputs
-- Motion-related QC metrics
-- DVARS and motion–DVARS correlation measures
-
-All metrics are evaluated using RBC-recommended thresholds.
+Computes framewise displacement (FD), DVARS, motion-DVARS correlation, and
+tSNR. Metrics are evaluated against RBC-recommended thresholds from Shafiei
+et al. (2024). Outputs follow XCP-style formatting.
 """