BrainAlign/ds003604-session-rdms

ds003604 session RDMs

Brain representational dissimilarity matrices for the ds003604 auditory language fMRI dataset, one per (task × session), so the fMRI preprocessing never has to be repeated.

12 of 12 cells present: Sem, Phon, Gram, Plaus × ses-5, ses-7, ses-9.

Each <Task>/session_rdm_<ses>.npz contains:

key	contents
rdm	the RDM, (n_stim, n_stim), correlation distance. 72×72 for Sem/Phon, 60×60 for Gram/Plaus (perceptual-control trials excluded)
stimuli	stimulus filenames, in RDM row/column order
stimulus_texts	the stimulus text, parallel to stimuli — use this if you are feeding a language model, not stimuli
trial_types	condition code per stimulus (e.g. S_H, P_R, G_G, SP_S)
semantic_categories	coarse category per stimulus
n_subjects, subject_ids	cohort behind the RDM (38–98 depending on cell)
metric, aggregation	correlation, and how subjects were combined

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⚠️ These RDMs are dominated by a scanner-run confound

Do not use them for representational similarity analysis without correcting this first.

In ds003604 each stimulus is presented in exactly one scanner run (for Phon, run-01 carries 48 of the 96 stimuli and run-02 the other 48). Run membership is therefore perfectly confounded with stimulus identity, and every cross-run stimulus pair also differs by that run's drift, baseline and scaling. Measured on these files:

"different run" predicts brain dissimilarity, Spearman rho:
    Gram   ses-5 +0.866   ses-7 +0.812   ses-9 +0.828
    Plaus  ses-5 +0.741   ses-7 +0.689   ses-9 +0.761
    Phon   ses-5 +0.562   ses-7 +0.488   ses-9 +0.624
    Sem    ses-5 +0.511   ses-7 +0.510   ses-9 +0.601

Meanwhile no stimulus property predicts them: trial type ≈ −0.02, text length ≈ 0, lexical overlap ≈ 0, in every cell.

These RDMs correlate across independent subject cohorts at rho 0.74–0.92 (different sessions of the same task), which looks like excellent reliability — but run assignment is fixed by the protocol and so repeats identically for every subject, meaning much of that reliability is the reliability of an acquisition artefact rather than of brain representation.

The fix

Z-score each voxel within run before combining runs. Verified on Phon/ses-5 rebuilt from 28 subjects' raw patterns:

standard RDM        vs run model:  rho = +0.562
within-run-normed   vs run model:  rho = -0.041      <- confound removed
standard            vs normed   :  rho = +0.287      <- they are largely different RDMs

That last line matters: correcting the confound does not nudge the RDM, it changes it.

Cohort size is not the issue — Sem/ses-7 rebuilt from 40 to 98 subjects agrees with the 40-subject version at rho 0.928.

After correction, alignment between these RDMs and a trained language model peaks at +0.022 (early layers, not significant), with a sensible layer profile but ≈0 magnitude. Evidence and scripts: BrainAlign/cdl-devai-results (diagnostics_run_confound, diagnostics_layerwise) and suchirsalhan/cdl-representations-brains-babylms (scripts/test_within_run_norm.py, scripts/run_confound_check.py).

The files here are published uncorrected, as produced by the pipeline, so that the correction is an explicit and visible choice rather than something baked in silently.