[Slices Segment] Menu
Use [Slices Segment] to segment the active 3D image slice into anatomical tissues, subcortical nuclei, perivascular spaces, or pathological lesions using 3D U-Net models and add each structure to Assign Regions. Available models update automatically for the selected species template, while skull stripping and 3D mesh extraction are in the Slices menu.
How slice segmentation works
Select a species template (human, rhesus, marmoset, rat, or mouse) in Assign Regions to populate [Slices Segment] (also opened by Segment… in the Assign Regions toolbar), and choose the target volume in the 3D viewport’s top-left slice selector. Contrast-flexible models work on any slice, whereas modality-specific models check the slice name (case-insensitive) for t1/mpr, t2/tse, or flair/t2f and otherwise disable with (need T1w), (need T2w), or (need FLAIR). Model weights download automatically on first use and add regions at the active slice’s native millimeter resolution and alignment with passive Type ... until changed to ROI, ROA, Seed, or End.
Human anatomy and tissue models
Shown when the human template is selected in Assign Regions.
| Menu item | Behavior |
|---|---|
| Segments human brain MRI into 32 anatomical regions—including cortex, white matter, ventricles, CSF, brainstem, thalamus, basal ganglia, hippocampus, and amygdala—at native slice resolution. Works on any slice regardless of MRI contrast or resolution. | |
| Segments unstripped human head MRI into 39 intracerebral and extracerebral head-tissue regions in Assign Regions. Works on any slice across contrasts, resolutions, and pathology. | |
| Segments unstripped human head MRI into 12 brain-tissue regions plus extracerebral head, skull, dura, and vessel regions. Works on any slice across contrasts, resolutions, and pathology. | |
| Segments unstripped human head MRI into the 12 brain and extracerebral head, skull, dura, and vessel regions of SIAM Model 2 (51.8MB) plus an abnormal-tissue anomaly region. Works on any slice across contrasts and resolutions. | |
| Segments whole-brain human MRI into 35 anatomical brain structures in Assign Regions using the GOUHFI 2.0 network. Works on any slice across MRI contrasts, resolutions, and field strengths. | |
Segments white-matter perivascular spaces (PVS) into Assign Regions. Requires a T2-weighted slice with t2 or tse in its name; otherwise disabled with (need T2w). |
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| Segments human brain MRI into five major tissue regions in Assign Regions. Enabled on any slice across T1w, T2w, FLAIR, and related structural contrasts. | |
Segments T1-weighted human brain MRI into five major tissue regions using a lightweight model. Requires t1 or mpr in the slice name; otherwise disabled with (need T1w). |
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Segments T2-weighted human brain MRI into five major tissue regions using a lightweight model. Requires t2 or tse in the slice name; otherwise disabled with (need T2w). |
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Segments human FLAIR MRI into five major brain-tissue regions using a lightweight model. Requires flair or t2f in the slice name; otherwise disabled with (need FLAIR). |
Human lesion and disease models
Listed below the human anatomy models when the human template is active.
| Menu item | Behavior |
|---|---|
Segments whole-tumor extent as a single combined Tumor region in Assign Regions. Enabled on any slice across T1w, contrast-enhanced T1w, T2w, and FLAIR; use U-Net Studio Human Tumor Lesion V2 (13MB) for separate tumor subcompartments. |
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| Segments multiple sclerosis (MS) lesions alongside major brain structures (19 regions total) into Assign Regions. Works on any slice across clinical MRI contrasts and scan qualities. | |
Segments brain tumors into separate Enhancing Tumor, Necrosis, and Peritumoral Edema regions alongside five surrounding brain-tissue regions. Enabled on any slice across T1w, contrast-enhanced T1w, T2w, and FLAIR. |
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Segments brain-tumor compartments and surrounding tissues on non-contrast T1-weighted MRI using a lightweight model. Requires t1 or mpr in the slice name; otherwise disabled with (need T1w). |
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Segments brain-tumor compartments on gadolinium contrast-enhanced T1-weighted MRI using a lightweight model. Requires t1 or mpr in the slice name ((need T1w) otherwise); confirm manually that the T1w scan is contrast-enhanced. |
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Segments brain tumors and peritumoral hyperintensity on FLAIR MRI using a lightweight model. Requires flair or t2f in the slice name; otherwise disabled with (need FLAIR). |
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| Segments acute or chronic stroke lesions into Assign Regions. Enabled on any slice across T1w, T2w, FLAIR, and related structural stroke MRI. | |
| Segments multiple sclerosis white-matter and parenchymal lesions into Assign Regions. Enabled on any slice across T1w, T2w, FLAIR, and related structural MRI. | |
Segments stroke lesions on human T1-weighted MRI using a lightweight model. Requires t1 or mpr in the slice name; otherwise disabled with (need T1w). |
Animal template models
Shown when rhesus, marmoset, rat, or mouse is selected as the template in Assign Regions.
| Menu item | Behavior |
|---|---|
Segments rhesus macaque brain MRI into tissue regions in Assign Regions. Shown for the rhesus template and enabled on any slice across contrasts. |
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Segments marmoset brain MRI into tissue regions in Assign Regions. Shown for the marmoset template and enabled on any slice across T1w, T2w, and FLAIR. |
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Segments T1-weighted marmoset brain MRI into tissue regions using a lightweight model. Shown for the marmoset template; requires t1 or mpr in the slice name ((need T1w) otherwise). |
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Segments T2-weighted marmoset brain MRI into tissue regions using a lightweight model. Shown for the marmoset template; requires t2 or tse in the slice name ((need T2w) otherwise). |
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Segments rat brain MRI into tissue regions in Assign Regions. Shown for the rat template and enabled on any slice across contrasts. |
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Segments T2-weighted rat brain MRI into tissue regions using a lightweight model. Shown for the rat template; requires t2 or tse in the slice name ((need T2w) otherwise). |
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Segments mouse brain MRI into tissue regions in Assign Regions. Shown for the mouse template and enabled on any slice across contrasts. |
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Segments T2-weighted mouse brain MRI into tissue regions using a lightweight model. Shown for the mouse template; requires t2 or tse in the slice name ((need T2w) otherwise). |
Practical recommendations and cautions
Prefer ~1 mm isotropic 3D structural scans over thick-slice 2D series, and verify slice-to-diffusion alignment ([Slices][Adjust Slice Registration…]) before segmenting because generated regions inherit the active slice’s registration. Multi-label models add empty (0-voxel) rows when a compartment is absent; always inspect generated boundaries across all three slice planes and clean up false-positive islands in the Region Edit menu before quantitative reporting or tract filtering.