Epilepsy MRI protocol
A routine brain will miss the subtle target of epilepsy imaging. This protocol is built around the hippocampus, with high-resolution slices angled specifically to the temporal lobe, to find mesial temporal sclerosis and small cortical lesions.
By the ScanFlo Editorial Team · Updated
In this section · Protocols
When this study is used
- New-onset or refractory seizures.
- Pre-surgical evaluation for epilepsy.
- Suspected mesial temporal sclerosis or focal cortical dysplasia.
Patient & coil positioning
- Head-first supine in a head coil; straight, no roll. Asymmetry ruins the side-to-side hippocampal comparison this exam depends on.
- Chin slightly tucked, centred on the glabella.
- Immobilise firmly; the thin high-resolution sequences are very motion-sensitive.
Localizer
Three-plane localizer, plus a routine brain survey (DWI, FLAIR, T2, T1) as the backbone. The dedicated coronal-oblique sequences are then angled to the hippocampi on the sagittal.
Sequence planning
For each sequence below you get the reference line the slice group follows, how much it covers, and why the sequence is in the protocol at all. Plan against the localizer, not by eye.
Coronal oblique T2 (thin)
Coronal obliquePlanning: Angle perpendicular to the long axis of the hippocampus (parallel to the brainstem) on the sagittal. Thin 2–3 mm slices, no gap, through the whole temporal lobe.
Why: Hippocampal signal and internal architecture: the core of mesial temporal sclerosis detection.
Coronal oblique FLAIR (thin)
Coronal obliquePlanning: Same angulation and coverage as the coronal T2.
Why: Bright hippocampal signal and cortical/subcortical lesions against nulled CSF.
Volumetric 3D T1 (MPRAGE)
3D / reformattedPlanning: Whole-brain isotropic acquisition; reformat along the hippocampal axis.
Why: Hippocampal volume asymmetry and subtle cortical dysplasia; morphometry.
Axial DWI + FLAIR
AxialPlanning: Routine AC–PC angulation.
Why: Excludes acute causes and completes the survey.
Representative parameters
Treat these as ranges. Field strength, coil and vendor all move the numbers. What must not move is understanding why each sits where it does.
| Sequence | Slice / gap | Matrix | Notes |
|---|---|---|---|
| Coronal T2 (thin) | 2–3 mm / 0% | 384+ | Perpendicular to hippocampi |
| Coronal FLAIR (thin) | 2–3 mm / 0% | 320+ | TI nulls CSF |
| 3D T1 MPRAGE | 1 mm isotropic | 256+ | Volumetry, reformats |
| DWI (EPI) | 4–5 mm | 128–192 | Rule out acute cause |
Artifacts & how to fix them
| Artifact | Typical cause | Mitigation |
|---|---|---|
| Asymmetric hippocampi | Rolled or tilted head | Reposition straight before scanning, not by angling alone |
| Partial volume on hippocampus | Slices too thick or off-axis | Thin slices, angled perpendicular to the hippocampal axis |
| Motion blur | Long thin-slice sequences | Firm immobilisation; parallel imaging to shorten |
| CSF flow on FLAIR | Temporal-horn pulsation | Flow compensation; verify against T2 |
What am I looking at?
You are not reporting the study, but recognising pathology helps you keep it in the field of view and know when to add a sequence or contrast. How the common findings read on the console:
| Finding | Sequence to check | How it reads |
|---|---|---|
| Mesial temporal sclerosis | Coronal T2/FLAIR | Small, bright hippocampus with lost internal architecture |
| Focal cortical dysplasia | 3D FLAIR / T1 | Blurred grey–white junction, thickened cortex, 'transmantle' sign |
| Hippocampal volume loss | 3D T1 reformats | Asymmetric size on side-by-side coronal reformats |
Review checklist
- Head straight, so the hippocampi are genuinely comparable left to right.
- Coronal obliques angled perpendicular to the hippocampal axis.
- Thin slices with no gap through both temporal lobes.
- Volumetric T1 acquired for reformatting and morphometry.
Mistakes that cost repeats
- Running only a routine brain and missing subtle mesial temporal sclerosis.
- A rolled head making one hippocampus look abnormally bright.
- Slices too thick to resolve hippocampal architecture.
- Skipping the volumetric T1 that quantifies asymmetry.
Common questions
- Why does an epilepsy protocol differ from a routine brain?
- It targets the hippocampus with thin, high-resolution coronal sequences angled perpendicular to the temporal lobe, plus a volumetric T1. A routine axial stack lacks the resolution and angulation to show mesial temporal sclerosis reliably.
- How are the coronal slices angled for epilepsy imaging?
- Perpendicular to the long axis of the hippocampus (in practice, parallel to the brainstem on the sagittal), so each slice cuts the hippocampus in true cross-section.
- Why is head symmetry so important here?
- The diagnosis often rests on comparing the two hippocampi. A rolled or tilted head makes one side look brighter or larger than the other, mimicking or masking pathology.
Try it in ScanFlo: Angle a coronal stack perpendicular to the hippocampal axis, then repeat it with a straight coronal, and compare how the hippocampus is cut. Only the angled view shows it in true cross-section, and that difference decides whether sclerosis is visible. See ScanFlo MRI →