Decoupling Parcellation from Classification: Systematic Benchmark of Fast Brain Segmentation Methods for Alzheimer's Disease Detection

Anatomical brain parcellations dominate rs-fMRI-based Autism Spectrum Disorder (ASD) classification, yet their rigid boundaries may fail to capture the idiosyncratic connectivity patterns that characterise ASD. We present a graph-based deep learning framework comparing anatomical (AAL, 116 ROIs) and functionally-derived (MSDL, 39 ROIs) parcellation strategies on the ABIDE I dataset. Our FSL preprocessing pipeline handles multi-site heterogeneity across 400 balanced subjects, with site-stratified 70/15/15 splits to prevent data leakage. Gaussian noise augmentation within training folds expands samples from 280 to 1,680. A three phase pipeline progresses from a baseline GCN with AAL (73.3% accuracy, AUC=0.74), to an optimised GCN with MSDL (84.0%, AUC=0.84), to a Graph Attention Network ensemble achieving 95.0% accuracy (AUC=0.98), outperforming all recent GNN-based benchmarks on ABIDE I. The 10.7-point gain from atlas substitution alone demonstrates that functional parcellation is the most impactful modelling decision. Gradient-based saliency and GNNExplainer analyses converge on the Posterior Cingulate Cortex and Precuneus as core Default Mode Network hubs, validating that model decisions reflect ASD neuropathology rather than acquisition artefacts. All code and datasets will be publicly released upon acceptance.

Deep learning models for Alzheimer disease (AD) classification routinely report near-perfect discrimination, yet few are shown to rest on AD-relevant neurobiology rather than on dataset artifacts, subject-level leakage, or non-brain image content. We present a fusion network combining T1 MRI and FDG PET across axial, coronal, and sagittal planes, trained on ADNI consists of 554 paired subjects. The fusion model reaches AUC 0.962, accuracy 0.909, and F1 0.891, competitive with recent 3D CNN and multimodal transformer systems at substantially lower cost. We first quantify how much modality, plane and slice geometry matter. A validation-only search over slice centres and neighbour spacings moves AUC by 0.180 for MRI and 0.078 for PET, selecting narrow spacing for MRI and wide spacing for PET, with the chosen coronal centres falling on the hippocampal body and on the posterior cingulate respectively. The contribution, however, is the evidence layer built around that number. Shortcut controls collapse the model to AUC 0.622 (silhouette), 0.608 (exterior), and 0.500 (blank), and a label-permutation null yields 0.456. Forward region-of-interest (ROI) ablation shows that masking medial temporal cortex in MRI and the posterior default-mode network (DMN) in PET produces the largest shift in the AD logit, while area-matched controls remain indistinguishable from that null. Reverse ROI ablation shows that the medial temporal lobe alone retains 89.2% of above-chance discrimination in MRI and the posterior DMN alone retains 79.0% in PET. A quantitative comparison of attribution methods shows occlusion sensitivity reaching 3.5-5.0* enrichment inside a priori AD regions against 0.10-0.43* in controls. Ablation and attribution independently establish a biologically correct double dissociation: hippocampal evidence is carried by MRI, posterior cingulate evidence by PET.

Deep networks trained on structural MRI for Alzheimer's disease (AD) staging often reach reasonable accuracy while attending to anatomically irrelevant regions, and multimodal models that add clinical tables frequently rely on variables that were used to assign the diagnostic label in the first place. We study both issues with a deliberately lightweight slice-based encoder (ResNet18 with a one-layer Transformer over slices) on 1,075 baseline T1-weighted scans from ADNI-1. First, we use FastSurfer segmentations as an anatomical reference: YOLOv8 models trained on segmentation-derived labels localize Alzheimer-relevant structures with mAP_50 above 0.96, and a Grad-CAM comparison shows that the image-only classifier frequently attends to the skull, orbits and background. Second, we adapt a CLIP-style image - tabular contrastive framework and organize ADNIMERGE variables along a label-leakage spectrum. Fusion with cognitive scores yields 87.3% three-way accuracy, which we treat as a leakage-driven upper bound rather than an imaging result; fusion with regional volumes yields 73.0%. We observe that the choice of contrastive target changes what the image encoder learns: on MCI vs. CN, the image-only head reaches 52.4% when the encoder is aligned to cognitive scores and 73.8% when aligned to volumes, although no tabular input is used at inference. Third, restricting the input to a per-subject crop of the medial temporal lobe raises image-only three-way accuracy from 58.7% to 65.1%. All results come from single runs on a small balanced test set, and we report confidence intervals and the protocol differences that prevent direct comparison with published numbers.