Supported modalities & formats
NeuXelec accepts any combination of the following imaging modalities:
- T1 MRI — reference volume, all other images are registered to this
- T2 MRI — registered to T1 with rigid transform
- CT — rigid registration (preserves electrode geometry)
- PET — rigid registration to T1
- SPECT ictal & interictal — for SISCOM computation
- Pial surfaces — left/right hemisphere meshes (FreeSurfer)
- Brain parcellations — FreeSurfer aparc+aseg or custom atlases
Accepted file formats: NIfTI (.nii, .nii.gz), DICOM folders (auto-converted), MGZ (FreeSurfer native).
ANTs coregistration
All modalities are registered to the T1 reference using ANTs (Advanced Normalization Tools) with rigid registration, preserving the geometry of all structures.
Transform matrices are saved for downstream use.
Automatic brain masking
NeuXelec uses template-based ANTs registration to generate a brain mask from the T1 volume. The mask constrains all downstream processing to brain tissue, improving coregistration quality and SISCOM accuracy.
Visual validation
After coregistration, use the built-in overlay viewer to inspect alignment quality for any pair of modalities. Adjust or re-run registration if needed — all original files remain untouched.
SISCOM computation
When both ictal and interictal SPECT scans are loaded and coregistered, NeuXelec computes SISCOM automatically: normalization → subtraction → z-score map → thresholded result.
Workflow
- Load T1 MRI (required) — all other modalities are optional
- Load any combination of CT, T2, PET, SPECT ictal/interictal
- Click "Perform coregistration" — progress shown per modality
- Inspect alignment in the overlay viewer
- Optionally load pial surfaces and parcellation atlases
- All coregistered files are saved to your project directory