Why align the axial stack to the genu and splenium?

Because comparability is diagnostic. A line along the under-surfaces of the genu and splenium of the corpus callosum runs nearly parallel to the AC–PC line, and either gives the same reproducible axial angle on every visit and every scanner, so follow-up exams compare slice for slice. Use the reference your department uses, every time.

In what order are the sequences scanned?

This routine runs the T2, T1 and FLAIR axials, then the sagittal and coronal T2, then DWI and SWI. Many departments move DWI and FLAIR earlier when the patient may not tolerate the whole exam, because DWI answers the most time-critical question: acute infarct. Follow your department's order; what must not vary is that every axial copies the same geometry.

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 20–32 axial slices at 4–5 mm thickness with a 10–40% gap, planned from above the vertex down to the foramen magnum. The count follows the head size.

Routine brain MRI protocol

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.

By the ScanFlo Editorial Team · Updated 12 October 2026

In this section · Protocols

Protocols/Brain

Video language

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 or cushions 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

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.

Axial T2 TSE

Axial

Planning: On the sagittal localizer, angle the block parallel to the genu and splenium of the corpus callosum; on the coronal, keep it perpendicular to the brain midline and the fourth ventricle. Cover the whole brain from the vertex to the foramen magnum, and check the FoV on the axial so nothing is cut off at the front or back.

Why: General anatomy, CSF spaces and the broadest pathology contrast in the exam. It is also the reference geometry every other axial copies.

Axial T1 TSE

Axial

Planning: Copy the T2 axial's slices (Copy Parameter → Slices) rather than re-planning by eye, so both stacks fall in the same place slice for slice.

Why: Anatomy with fat and subacute blood bright and CSF dark; the baseline for any post-contrast comparison.

Axial T2 FLAIR

Axial

Planning: Copy the T2 axial's slices. Check that the inversion time nulls CSF at your field strength.

Why: Periventricular and cortical lesions, gliosis and oedema against suppressed CSF. This is the workhorse of demyelination and small-vessel disease.

Sagittal T2 TSE

Sagittal

Planning: On the axial and the coronal, keep the block parallel to the brain midline (and the fourth ventricle on the coronal). Cover from one temporal lobe to the other and check the FoV on the sagittal.

Why: Midline anatomy (corpus callosum, pituitary region, aqueduct and posterior fossa) in the plane the axial stack cannot show.

Coronal T2 TSE

Coronal

Planning: On the sagittal, parallel to the pons and medulla oblongata (along the brainstem); on the axial, perpendicular to the midline. Cover from the frontal sinus to the occipital protuberance and check the FoV on the coronal.

Why: A second orthogonal view that resolves partial-volume ambiguity from the axial stack, especially in the temporal lobes and ventricles.

Axial DWI + ADC

Axial

Planning: Copy the T2 axial's slices so DWI compares slice for slice; b = 0 and 1000 s/mm², with the ADC map calculated.

Why: Acute infarct, abscess and highly cellular tumour via restricted diffusion: bright on DWI and dark on ADC.

Axial SWI

Axial

Planning: A 3D sequence with its own thin slices: match its centre and angle to the T2 axial and check it covers the whole brain.

Why: Haemorrhage, calcification and microbleeds through susceptibility contrast. It is the most sensitive sequence for blood and calcium.

In the video

The video scans ScanFlo's Brain Routine case 4. The angles are that patient's, so follow the landmarks, not the numbers.
Axial T2: 21 slices, 5 mm, 36% gap, FoV 231 mm, phase encoding right to left; tilted about 1° on the sagittal and 5.5° on the coronal.
T2 TSE TR 4370 / TE 94 ms; T1 TSE TR 500 / TE 11 ms.
The sagittal is tilted about 7° on the coronal; the coronal leans about 10° forward along the brainstem.
T1, FLAIR and DWI copy the T2 axial with Copy Parameter → Slices; SWI keeps its own thin 3D slices.
The whole exam takes about 11 minutes; the video shows the scan as a time-lapse.

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	TR (ms)	TE (ms)	Slice / gap	Notes
T2 TSE	3000–6000	80–120	4–5 mm / 10–40%	Long/long; most pathology
T1 TSE / SE	400–650	8–15	4–5 mm / 10–40%	Short/short; anatomy, subacute blood
FLAIR	8000–11000	80–140	4–5 mm / 10–40%	TI ≈ 2000–2500 ms nulls CSF
DWI (EPI)	3000–6000	60–100	4–5 mm / 10–40%	b = 0 and 1000 s/mm²
SWI (3D GRE)	27–50	20–40	1.5–2 mm, no gap	Low flip; susceptibility-sensitive

Artifacts & how to fix them

Artifact	Typical cause	Mitigation
Motion / ghosting	Restless patient, long sequence late in exam	Immobilise and reassure; repeat the affected sequence; 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 (when given)	Enhances white, with bright surrounding oedema on T2 and FLAIR
Abscess	DWI	Restricts and stays bright, like an infarct
Demyelination	FLAIR	Bright ovoid spots touching the corpus callosum; add a sagittal FLAIR when MS is the question

Review checklist

Whole brain covered vertex to foramen magnum, no gap at the convexity.
Left–right symmetry on the axial stack. Asymmetry here 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 (not parallel to the genu–splenium line) make follow-up comparison unreliable.
A vertex gap from starting the stack a slice too low.
FLAIR with the wrong inversion time, so CSF stays bright and the sequence becomes a noisy T2.
Planning the T1, FLAIR and DWI by eye instead of copying the T2 axial. The stacks then no longer compare slice for slice.

Common questions

Why align the axial stack to the genu and splenium?: Because comparability is diagnostic. A line along the under-surfaces of the genu and splenium of the corpus callosum runs nearly parallel to the AC–PC line, and either gives the same reproducible axial angle on every visit and every scanner, so follow-up exams compare slice for slice. Use the reference your department uses, every time.
In what order are the sequences scanned?: This routine runs the T2, T1 and FLAIR axials, then the sagittal and coronal T2, then DWI and SWI. Many departments move DWI and FLAIR earlier when the patient may not tolerate the whole exam, because DWI answers the most time-critical question: acute infarct. Follow your department's order; what must not vary is that every axial copies the same geometry.
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 20–32 axial slices at 4–5 mm thickness with a 10–40% gap, planned from above the vertex down to the foramen magnum. The count follows the head size.

Try it in ScanFlo: Load the head routine case. Plan the axial T2 parallel to the genu–splenium line and copy it to the T1 and FLAIR, then plan a second T2 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. See ScanFlo MRI →

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