Supported modalities & formats
NeuXelec accepts any combination of the following imaging modalities. All coregistrations are performed using MRI 1 as the reference volume.
- MRI 1: reference volume, all other images are registered to this one
- MRI 2: registered to MRI 1 with rigid transform (accepts any MRI modality: T1, T2, FLAIR, etc.)
- CT: rigid registration, preserves electrode geometry
- PET: rigid registration to MRI 1
- 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 MRI 1 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 MRI 1 volume. The mask constrains all downstream processing to brain tissue, improving coregistration quality and SISCOM accuracy.
File status tracking
Each imported file displays its coregistration status in real time: Missing, Loaded, or Coregistered. You can see at a glance which modalities have been aligned and which still need processing, without having to re-run the full pipeline.
Save coregistered images
Once coregistration is complete, all aligned volumes can be exported directly from the interface. Each coregistered file is saved in NIfTI format to your project directory, ready for further analysis or sharing with collaborators.
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 MRI 1 (required): all other modalities are optional
- Load any combination of CT, MRI 2, PET, SPECT ictal/interictal
- Monitor each file's status: Pending, In progress, Done
- Click "Perform coregistration": progress shown per modality
- Inspect alignment in the overlay viewer
- Save coregistered images to your project directory
- Optionally load pial surfaces and parcellation atlases