Resources/Protocols
Brain MRI protocols
The highest-volume region in MRI, and where console fundamentals are built. Every specialised brain protocol is the routine exam plus a deliberate change.
Brain imaging teaches the discipline the rest of MRI depends on: consistent angulation, complete coverage, and a sequence order that puts the most time-critical information first. Learn the routine survey properly and stroke, epilepsy and tumour protocols stop being separate exams — they become variations you can reason about.
Deep-dive protocol guides
Full step-by-step protocols — positioning, per-sequence planning, parameters, artifacts and a review checklist for each study:
Studies in this region
- Routine brain
- Stroke
- Epilepsy
- Parkinson protocol
- Cranial nerves
- Inner ear (IAC)
- CP angle
- Pituitary
- Orbits
- CSF flow
- Spectroscopy
- Perfusion
- Brain mapping
- Tractography (DTI)
- Functional MRI
- MR angiography
- MR venography
- Vessel wall imaging
- Neonatal quiet protocols
- Contrast MPRAGE
Planning
- Align axial stacks to the AC–PC line on the sagittal localizer so follow-up exams compare slice-for-slice.
- Cover vertex to foramen magnum with no gap at the convexity — that is where subtle pathology hides from careless planning.
- Correct head roll in the slice angulation, not by repositioning a settled patient.
- Use an anterior–posterior phase direction on axials so flow and motion ghosts land outside the hemispheres.
- For pituitary, IAC and orbit studies, drop to thin slices and a small field of view centred on the target — resolution beats coverage here.
Sequences by study
| Study | Core additions to the routine | Why |
|---|---|---|
| Routine brain | DWI/ADC, FLAIR, T2 TSE, T1, T2*/SWI | Broad contrast variety for general survey |
| Stroke | DWI early, SWI, MRA, perfusion if available | Infarct age, hemorrhage exclusion, vessel status |
| Epilepsy | Thin coronal T2/FLAIR angled to hippocampi, 3D T1 | Mesial temporal sclerosis and subtle cortical lesions |
| Pituitary | Thin sagittal & coronal T1 pre/post, dynamic contrast | Microadenoma detection needs resolution and timing |
| IAC / CP angle | Heavily T2-weighted 3D thin-slice, post-contrast T1 | Nerve and small tumour visualisation |
| Orbits | Fat-suppressed T2 and post-contrast T1, thin slices | Fat suppression separates lesion from orbital fat |
| MRA / MRV | Time-of-flight or contrast angiography, MIP reconstructions | Arterial or venous anatomy without catheters |
Representative parameters
Ranges, not commandments — field strength, coil and vendor move the numbers. What must not move is understanding why each sits where it does.
| Sequence | TR (ms) | TE (ms) | Notes |
|---|---|---|---|
| T1 SE | 400–650 | 8–15 | Short/short — anatomy and subacute blood |
| T2 TSE | 3000–6000 | 80–120 | Long/long — most pathology |
| FLAIR | 8000–11000 | 80–140 | TI ≈ 2000–2500 ms nulls CSF |
| DWI (EPI) | 3000–6000 | 60–100 | b = 0 and 1000 s/mm² |
| T2* / SWI | 600–800 | 15–25 | Low flip angle; susceptibility-sensitive |
Mistakes that cost repeats
- Un-angled axials that make follow-up comparison unreliable.
- A vertex gap from starting the stack a slice too low.
- FLAIR with the wrong inversion time — CSF stays bright and the sequence becomes a noisy T2.
- Leaving motion-intolerant sequences (DWI, FLAIR) until last, when the patient is least still.
Common questions
- Why align brain axials to the AC–PC line?
- Because comparability is diagnostic. Slices angled to the anterior–posterior commissure line reproduce the same anatomy across visits and scanners, so follow-up studies can be compared directly.
- Why does DWI come early in a brain protocol?
- Diffusion answers the most time-critical question — acute infarct — and tolerates motion least. If the exam ends early, DWI plus FLAIR already carries most of the clinical value.
- What makes an epilepsy protocol different from a routine brain?
- Angulation and resolution. Thin coronal T2 and FLAIR angled perpendicular to the long axis of the hippocampi, plus a volumetric T1, target mesial temporal sclerosis that a routine axial stack can miss.
- Why is dynamic contrast used for pituitary imaging?
- A microadenoma often enhances at a different rate than normal gland tissue. Imaging repeatedly during contrast arrival captures that difference, which a single post-contrast series can miss.
Try it in ScanFlo: Plan a routine brain axial stack aligned to AC–PC, then a second deliberately mis-angled by 15°, and scan both. Compare how the ventricles and basal ganglia change shape — that difference is why the alignment standard exists.