i
Draw the lesion on at least two slices in the selected orientation. Interp finds the first and last non-empty slices, fills the slices between them with NiiVue mask interpolation, and thresholds the result back to lesion voxels.
70%
Mask approval requiredReview the lesion mask before analysis continues.
Direct lesion overlap
i
Atlas labels listed here contain lesion voxels directly. Lesion % is the share of lesion voxels in each label.
Atlas label
Voxels
Lesion %
Functional associations from direct lesion overlap
i
Exploratory literature terms are available for selected atlas labels; they are not clinical predictions.
Term
Score
Atlas label drivers
Run analysis first to enable thresholding.
Connectivity-map effects
i
Atlas labels listed here contain voxels surviving the thresholded connectivity map. Map % is the share of thresholded map voxels in each label.
Atlas label
Voxels
Map %
Functional associations from connectivity-map effects
i
Exploratory literature terms are available for selected atlas labels; they are not clinical predictions.
Term
Score
Atlas label drivers
About CALMaR
CALMaR
Co-designed Automated Lesion Mapping and Reporting.
This app loads a structural T1 (or a manual MNI-aligned lesion mask) locally, runs the CALMaR lesion mapping chain in the browser, and never uploads patient data.
The pipeline: SynthStrip brain extraction → SynthStroke baseline lesion segmentation → SynthMorph deformable registration to MNI152 (1603 1mm) → affine-aware resample to the selected atlas grid → atlas overlap → group-FC weighted-sum → threshold + cluster cleanup. All stages are exposed as individual buttons under Advanced controls; Run analysis chains them in one click.
Background execution is possible if this site is added under "Always keep these sites active" in your browser settings.
Version
Application
Privacy
Your data remains on your device.
Uploaded images and masks are read into browser memory for local viewing and analysis.
What this means
No patient image data, lesion masks, voxel values, screenshots, or generated outputs are uploaded by the app.
Atlas and model assets may be fetched by the browser when a workflow needs them.
Downloaded result files are created locally from browser memory.
Third-party services
Static app files and public atlas assets may be served from external hosting, but patient-derived files are not sent to those services by the analysis code. The Neurodesk hosting layer records page views only, unless your browser sends Do Not Track or Global Privacy Control. It does not send custom events, patient images, masks, voxel values, screenshots, generated outputs, filenames, or analysis results to Google Analytics.