filtering

Applies temporal high-pass, low-pass, and band-pass filtering to denoise preprocessed fMRI BOLD time series.

89|5|Updated Mar 25, 2026
One-click install
npx skills add https://github.com/CUHK-AIM-Group/NeuroDiscovery --skill filtering-cuhk-aim-group
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: filtering
Source: https://github.com/CUHK-AIM-Group/NeuroDiscovery/tree/main/skills/filtering
Command: npx skills add https://github.com/CUHK-AIM-Group/NeuroDiscovery --skill filtering-cuhk-aim-group

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve? Raw fMRI BOLD time series contain unwanted frequency content and noise that corrupt downstream connectivity, decoding, and statistical analyses. This Skill provides model-level guidance for classical temporal filtering workflows, producing denoised BOLD images and cleaned ROI time series without deep-learning methods. ## Core Features & Use Cases - Temporal Filtering Routes: Apply high-pass, low-pass, or band-pass filtering to preprocessed BOLD time series using a specified TR and frequency band. - Confound-Aware Cleaning: Optionally combine filtering with confound regression, standardization, and masking for cleaner voxel-wise or ROI-wise signals. - Delegation Workflow: Coordinates with fmri-skill for preprocessing planning and nilearn-tool for concrete filtering execution and cleaned image export. - Use Case: A researcher with preprocessed resting-state fMRI data wants to retain the 0.01-0.08 Hz band before functional connectivity analysis; this Skill guides the band-pass filtering run and exports the denoised image plus QC summaries. ## Quick Start Ask the assistant to band-pass filter your preprocessed resting-state BOLD image between 0.01 and 0.08 Hz with TR 2.0 and export the denoised image to a run_models_output directory.

Frequently Asked Questions about filtering

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I band-pass filter resting-state fMRI data?

Band-pass filtering of resting-state fMRI typically retains the 0.01-0.08 Hz range using a preprocessed BOLD image and its TR. This Skill delegates execution to nilearn-tool, which applies the filter and exports a denoised image plus cleaned time series.

What inputs are required for fMRI temporal filtering?

Temporal filtering requires a preprocessed BOLD image and the repetition time (TR). Optional inputs include a confounds TSV, a brain mask, high-pass and low-pass frequency settings, and standardization or smoothing options.

Should I filter fMRI data before or after preprocessing?

Filtering should run after standard preprocessing such as motion correction and normalization. If images are not yet preprocessed, delegate to fmri-skill first, since filtering raw data can amplify artifacts rather than remove them.

Can temporal filtering remove meaningful brain signals?

Yes, over-aggressive filtering can remove task-related or physiological signals, especially in task-fMRI designs. Filtering parameters depend on TR and study design, so they should be chosen carefully and reported in downstream analyses.

When should I use classical filtering instead of deep-learning denoising?

Classical temporal filtering is preferred when you want a transparent, interpretable denoising baseline focused on frequency selection. It suits workflows needing standardized temporal cleaning before ROI extraction, connectivity, or decoding without learned models.