Resources/Protocols
Routine brain (MRI head)
The general brain survey and the exam every other head protocol is built on. Master its positioning, planning lines and sequence order and the specialised studies become deliberate variations rather than new exams.
When this study is used
- Headache, first seizure, new confusion or altered mental state.
- Suspected space-occupying lesion or raised intracranial pressure.
- Non-specific neurology where broad contrast coverage is needed.
- Follow-up imaging when no dedicated protocol is indicated.
Patient & coil positioning
- Patient head-first and supine, in a dedicated head or head–neck coil.
- Immobilise the head with pads so the interpupillary line is horizontal and there is no roll.
- Centre the alignment light on the glabella (roughly the nasion–brow).
- Give the patient the alarm ball and hearing protection; explain the acoustic noise before the first sequence.
Localizer
Acquire a three-plane localizer (axial, sagittal, coronal) and confirm the mid-sagittal slice truly bisects the brain — every planning line below is drawn on these images, so a rolled or off-centre localizer propagates error into the whole exam.
Sequence planning
Each sequence below lists how the slice group is positioned — the reference line it follows, its coverage, and why it earns its place in the protocol. Plan against the localizer, not by eye.
Axial DWI + ADC
AxialPlanning — Angle parallel to the AC–PC line on the sagittal localizer; cover vertex to foramen magnum. Plan first and scan early — it answers the most time-critical question and tolerates motion least.
Why — Acute infarct, abscess and highly cellular tumour via restricted diffusion, confirmed against the ADC map.
Axial T2 FLAIR
AxialPlanning — Same AC–PC angulation and coverage as the DWI so the two compare slice-for-slice. Verify the inversion time nulls CSF on the localizer field strength.
Why — Periventricular and cortical lesions, gliosis and oedema against suppressed CSF — the workhorse of demyelination and small-vessel disease.
Axial T2 TSE
AxialPlanning — Parallel to the genu and splenium of the corpus callosum, checked in two perpendicular planes; whole brain, no vertex gap.
Why — General anatomy, CSF spaces and the broadest pathology contrast in the exam.
Sagittal T1 SE/TSE
SagittalPlanning — Aligned to the interhemispheric fissure on the axial and coronal localizers so slices run true mid-line outward.
Why — Midline anatomy, corpus callosum, pituitary region, marrow signal and subacute blood.
Coronal T2 or FLAIR
CoronalPlanning — Perpendicular to the AC–PC line; angled to the target when a specific structure (temporal lobes, ventricles) is in question.
Why — A second orthogonal view that resolves partial-volume ambiguity from the axial stack.
Axial T2* GRE or SWI
AxialPlanning — Match the axial coverage; low flip angle. Keep it away from the very end of the exam if the patient is restless.
Why — Haemorrhage, calcification and microbleeds through susceptibility contrast.
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) | Slice / gap | Notes |
|---|---|---|---|---|
| T1 SE | 400–650 | 8–15 | 4–5 mm / 10–30% | Short/short — anatomy, subacute blood |
| T2 TSE | 3000–6000 | 80–120 | 4–5 mm / 10–30% | Long/long — most pathology |
| FLAIR | 8000–11000 | 80–140 | 4–5 mm / 10–30% | TI ≈ 2000–2500 ms nulls CSF |
| DWI (EPI) | 3000–6000 | 60–100 | 4–5 mm / 10–30% | b = 0 and 1000 s/mm² |
| T2* / SWI | 600–800 | 15–25 | 4–5 mm | Low flip; susceptibility-sensitive |
Artifacts & how to fix them
| Artifact | Typical cause | Mitigation |
|---|---|---|
| Motion / ghosting | Restless patient, long sequence late in exam | Front-load DWI/FLAIR; reassure; consider PROPELLER/BLADE |
| Susceptibility | Air–bone interfaces, dental work, EPI DWI | Spin echo where possible; shorten TE; wider bandwidth |
| CSF flow | Pulsatile CSF in aqueduct/ventricles on FLAIR | Flow compensation; check against T2 |
| Chemical shift | Fat–water at high bandwidth mismatch | Widen receive bandwidth or fat-suppress |
| Wrap-around | Head wider than the phase FOV | Enlarge FOV or enable phase oversampling |
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 |
|---|---|---|
| Acute stroke | DWI + ADC | Bright on DWI, dark on ADC (true restriction) |
| Tumour | T1 post-contrast | Enhances white, often with dark surrounding oedema on T2 |
| Abscess | DWI | Restricts and stays bright, like an infarct |
| Demyelination | Sagittal FLAIR | Bright ovoid spots touching the corpus callosum |
Review checklist
- Whole brain covered vertex to foramen magnum, no gap at the convexity.
- Left–right symmetry on the axial stack — asymmetry means a rolled plan, not pathology.
- Grey–white differentiation clear on T1 and T2.
- FLAIR CSF fully nulled; if bright, the TI is wrong for the field strength.
- DWI and ADC agree — true restriction is bright on DWI and dark on ADC.
- Laterality labelled and verified against the localizer before filming.
Mistakes that cost repeats
- Un-angled axials cut oblique to AC–PC, making 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 the motion-intolerant sequences (DWI, FLAIR) until last.
Common questions
- Why align the axial stack to the AC–PC line?
- Because comparability is diagnostic. Slices angled to the anterior–posterior commissure line reproduce the same anatomy on every visit and every scanner, so follow-up exams compare slice-for-slice.
- Why does DWI come first in a routine brain protocol?
- It answers the most time-critical question — acute infarct — and tolerates motion the least. If the exam ends early, DWI plus FLAIR already carries most of the clinical value.
- What inversion time nulls CSF on FLAIR?
- Roughly 2000–2500 ms at common field strengths. If CSF stays bright, the TI is wrong for your field strength — correct it before repeating the sequence.
- How many slices cover an adult brain?
- About 24–32 axial slices at 4–5 mm thickness with a 10–30% gap, planned from above the vertex down to the foramen magnum.
Try it in ScanFlo: Load the head routine case. Plan an 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.