skills-comm

Validate brain extraction / skull stripping results. Generate a QC PNG mosaic, perform AI visual evaluation against a structured rubric, and produce a matching human verification form for reliability comparison. Invoke after brain extraction completes, or standalone on any existing brain mask with "check brain extraction", "QC the mask", "validate skull strip", "review brain extraction", "evaluate the mask", or "brain-extraction-qc". Also invoke when the user references a file ending in `_brain.nii.gz`, `_mask.nii.gz`, or `_brain_mask.nii.gz` and asks to check, review, or validate it.

Perform brain extraction (skull stripping) on an MRI image in a portable neuroimaging workflow. Invoke on "skull strip", "brain extraction", "remove skull", "strip the brain", "BET", "antsBrainExtraction", "mri_synthstrip", "HD-BET", "3dSkullStrip", "synthstrip", "brain mask", "create brain mask", "whole brain mask", "mask the brain", "strip the skull", or "brain-extraction". Also invoke when the user wants to isolate brain tissue, remove non-brain voxels, or prepare a brain mask for downstream registration or segmentation.

Validate brain extraction / skull stripping results. Generate a QC PNG mosaic, perform AI visual evaluation against a structured rubric, and produce a matching human verification form for reliability comparison. Invoke after brain extraction completes, or standalone on any existing brain mask with "check brain extraction", "QC the mask", "validate skull strip", "review brain extraction", "evaluate the mask", or "brain-extraction-qc". Also invoke when the user references a file ending in `_brain.nii.gz`, `_mask.nii.gz`, or `_brain_mask.nii.gz` and asks to check, review, or validate it.

Perform brain extraction (skull stripping) on an MRI image in the Neurodesk environment. Invoke on "skull strip", "brain extraction", "remove skull", "strip the brain", "BET", "antsBrainExtraction", "mri_synthstrip", "HD-BET", "3dSkullStrip", "synthstrip", "brain mask", "create brain mask", "whole brain mask", "mask the brain", "strip the skull", or "brain-extraction". Also invoke when the user says they want to isolate brain tissue, remove non-brain voxels, or prepare a brain mask for downstream registration or segmentation.

Auto-invoke when the user wants to obtain a copy of a dataset from a URL or path, install a dataset, add a nested subdataset, or link external data as input to a project. Trigger on "clone a dataset", "get a copy of", "install dataset", "add subdataset", "link this data as input", or /datalad-clone. Use instead of `git clone` when working with DataLad datasets. Do NOT trigger for plain git repos without DataLad context.

Auto-invoke when about to execute a command inside a container (Singularity .sif file, Apptainer image, Docker image) that produces output files inside a DataLad dataset. Trigger on "run in container", "run with Singularity", "run with Apptainer", "run with Docker", "containerized analysis", "remove a container", "unregister container", or /datalad-container-run. Records both the command and the container image in dataset provenance. Do NOT trigger for bare datalad run commands without a container — use datalad-run for those.

Auto-invoke when the user needs to set up credentials for a DataLad remote, gets an authentication error pushing to GitHub/OSF/S3/Figshare, or asks how to store tokens for DataLad siblings. Trigger on "set up credentials", "configure token", "authentication error", "credential error", "how do I authenticate", "store my GitHub token for DataLad", "OSF token", "S3 credentials", or /datalad-credentials. Do NOT trigger for general SSH key setup or non-DataLad credential management.

Auto-invoke when a user cannot open a file because content is missing or shows as a broken symlink, wants to download annexed file content, fetch data from a sibling, or initialize an absent subdataset. Trigger on "get this file", "download content", "fetch data", "retrieve", "I can't open this file", "content missing", "file is empty", "broken symlink", or /datalad-get. Do NOT trigger for plain file copies or downloads unrelated to DataLad datasets.

Create a new DataLad dataset with YODA layout, or initialize provenance tracking in an existing directory. Trigger on "create a new DataLad dataset", "set up YODA dataset", "initialize data provenance tracking", "start a datalad project", or /datalad-init. Does NOT trigger for saving changes (use datalad-save) or running commands (use datalad-run).

Auto-invoke when the user wants to browse dataset history, find what command produced a specific output, inspect recorded run provenance, or audit past analyses. Trigger on "show run history", "what command produced this", "browse dataset history", "find the run that made this file", "show provenance", "list recorded runs", "what was the last run", or /datalad-log. Do NOT trigger for running new commands (use datalad-run) or replaying existing runs (use datalad-run's rerun section).

Auto-invoke when the user wants to transfer saved dataset state to a remote, publish a dataset, upload annexed content to a sibling, share changes with collaborators, or push to GitHub, OSF, or other storage. Trigger on "push to remote", "publish dataset", "upload to sibling", "share changes", "push to GitHub", "send to storage", or /datalad-push. Do NOT trigger for plain git push in repos without DataLad context.

Auto-invoke when about to execute a script, pipeline, or transformation that reads input data files and writes output files — e.g., `python analysis.py`, `bash process.sh`, neuroimaging tools (fMRIPrep, MRIQC, FSL, FreeSurfer), or any shell command that produces result files in a DataLad dataset. Also trigger on "run with provenance", "track this command", "record this analysis", "replay this run", "rerun a recorded command", "download this file with provenance", "record download", or /datalad-run. Do NOT trigger for commands that produce no output files (git log, ls, exploratory queries).

Auto-invoke inside a DataLad dataset (.datalad/ present) when the user asks what has changed, what is modified, what files are untracked, or what the current dataset state is. Trigger on "what changed", "check state", "show modified", "what's untracked", "dataset status", or /datalad-status. Read-only — never modifies any files.

Auto-invoke inside a DataLad dataset (.datalad/ present) when the user wants to free disk space by dropping annexed content, remove a file from the dataset entirely, stop tracking a file, or unlock an annexed file for in-place editing. Trigger on "drop file content", "free disk space", "untrack file", "remove from dataset", "stop tracking", "delete this file from the dataset", "unlock this file", "I need to edit an annexed file", "make this file writable", or /datalad-untrack. Do NOT trigger for plain file deletion outside a DataLad dataset.

Auto-invoke when the user wants to fetch changes from a sibling, sync a dataset from a remote, pull the latest version of a dataset, or update from a collaborator's push. Trigger on "pull updates", "sync from remote", "get latest version", "update from sibling", "someone pushed new data", "fetch upstream changes", or /datalad-update. Do NOT trigger for plain git fetch/pull in repos without DataLad context.

Monitor SLURM/PBS/LSF jobs, tail logs live, detect errors immediately as they appear in log output, cancel the job on fatal error so the user can iterate fast, and report status. Invoke when the user asks to "check my jobs", "monitor", "what's running", "did it finish", "job status", "check logs", "is it done", or after any sbatch/qsub submission. Also invoke proactively after every job submission — the default behavior is to immediately start watching logs for errors.

Execute ComBat-family harmonization on a feature matrix. Submit the harmonization script to a job scheduler, monitor progress, and validate that harmonization completed successfully. Invoke when the user says "run harmonization", "execute ComBat", "submit harmonization job", "apply batch correction", or when a harmonization script exists and needs to be run. Also invoke after generating a harmonization strategy to handle the execution step.

Analyze multi-site neuroimaging feature data and recommend the optimal ComBat-family harmonization method. Covers standard ComBat, ComBat-GAM, ComBat-Harmonize (longitudinal), CovBat, and RELIEF. Invoke when the user asks about "harmonizing features", "site correction", "batch effect removal", "ComBat", "harmonization method", "scanner effect", "multi-site harmonization", or "which harmonization to use". Also invoke when the user has a feature matrix (edges, thickness, volumes, connectivity) from multiple sites and needs to decide how to harmonize.

Find resting-state fMRI data in a directory, extract ROI time series using a brain atlas/parcellation, compute functional connectivity matrices (Pearson or partial correlation), and save them as ready-to-harmonize feature matrices. Invoke when the user asks for "functional connectivity", "FC matrices", "connectome generation", "resting state correlation", "parcellate fMRI", "extract time series", "atlas-based connectivity", or "generate connectomes". Also invoke when the user mentions rs-fMRI combined with any atlas name (Schaefer, Harvard-Oxford, AAL, DiFuMo, etc.) or when they need to preprocess raw BOLD for connectivity analysis without a full pipeline.

Visual quality control for ComBat-family harmonization results. Generate PCA/UMAP plots colored by site before and after harmonization, heatmap comparisons, variance explained by site, and a summary report. Invoke when the user asks for "harmonization QC", "check harmonization", "visualize ComBat results", "PCA before after harmonization", "evaluate site correction", "does harmonization work", or "validate batch correction". Also invoke after any harmonization completes to verify the results are meaningful.

Assist with the nipoppy CLI for managing neuroimaging datasets. Use when the user asks about nipoppy commands, setting up a nipoppy dataset, organizing DICOM files, running BIDS conversion (bidsify), executing processing pipelines (process, fMRIPrep, MRIQC), tracking pipeline status (track-processing), extracting imaging-derived phenotypes (extract/IDPs), or managing the pipeline catalog (pipeline install/search/ upload/validate). Also invoke for /nipoppy-cli or when a manifest.tsv or nipoppy config.json is present.

Perform brain extraction (skull stripping) on an MRI image in the Neurodesk environment. Invoke on "skull strip", "brain extraction", "remove skull", "strip the brain", "BET", "antsBrainExtraction", "mri_synthstrip", "HD-BET", "3dSkullStrip", "synthstrip", "brain mask", "create brain mask", "whole brain mask", "mask the brain", "strip the skull", or /brain-extraction. Also invoke when the user says they want to isolate brain tissue, remove non-brain voxels, or prepare a brain mask for downstream registration or segmentation.

Perform brain extraction (skull stripping) on an MRI image in the Neurodesk environment. Invoke on "skull strip", "brain extraction", "remove skull", "strip the brain", "BET", "antsBrainExtraction", "mri_synthstrip", "HD-BET", "3dSkullStrip", "synthstrip", "brain mask", "create brain mask", "whole brain mask", "mask the brain", "strip the skull", or "brain-extraction". Also invoke when the user says they want to isolate brain tissue, remove non-brain voxels, or prepare a brain mask for downstream registration or segmentation.

Perform brain extraction (skull stripping) on an MRI image in the Neurodesk environment. Invoke on "skull strip", "brain extraction", "remove skull", "strip the brain", "BET", "antsBrainExtraction", "mri_synthstrip", "HD-BET", "3dSkullStrip", "synthstrip", "brain mask", "create brain mask", "whole brain mask", "mask the brain", "strip the skull", or "brain-extraction". Also invoke when the user says they want to isolate brain tissue, remove non-brain voxels, or prepare a brain mask for downstream registration or segmentation.

Perform brain extraction (skull stripping) on an MRI image in the Neurodesk environment. Invoke on "skull strip", "brain extraction", "remove skull", "strip the brain", "BET", "antsBrainExtraction", "mri_synthstrip", "HD-BET", "3dSkullStrip", "synthstrip", "brain mask", "create brain mask", "whole brain mask", "mask the brain", "strip the skull", or "brain-extraction". Also invoke when the user says they want to isolate brain tissue, remove non-brain voxels, or prepare a brain mask for downstream registration or segmentation.

Validate brain extraction / skull stripping results. Generate a QC PNG mosaic, perform AI visual evaluation against a structured rubric, and produce a matching human verification form for reliability comparison. Invoke after brain extraction completes, or standalone on any existing brain mask with "check brain extraction", "QC the mask", "validate skull strip", "review brain extraction", "evaluate the mask", or "brain-extraction-qc". Also invoke when the user references a file ending in `_brain.nii.gz`, `_mask.nii.gz`, or `_brain_mask.nii.gz` and asks to check, review, or validate it.

Validate brain extraction / skull stripping results. Generate a QC PNG mosaic, perform AI visual evaluation against a structured rubric, and produce a matching human verification form for reliability comparison. Invoke after brain extraction completes, or standalone on any existing brain mask with "check brain extraction", "QC the mask", "validate skull strip", "review brain extraction", "evaluate the mask", or /brain-extraction-qc. Also invoke when the user references a file ending in `_brain.nii.gz`, `_mask.nii.gz`, or `_brain_mask.nii.gz` and asks to check, review, or validate it.

Validate brain extraction / skull stripping results. Generate a QC PNG mosaic, perform AI visual evaluation against a structured rubric, and produce a matching human verification form for reliability comparison. Invoke after brain extraction completes, or standalone on any existing brain mask with "check brain extraction", "QC the mask", "validate skull strip", "review brain extraction", "evaluate the mask", or "brain-extraction-qc". Also invoke when the user references a file ending in `_brain.nii.gz`, `_mask.nii.gz`, or `_brain_mask.nii.gz` and asks to check, review, or validate it.