Anatomy of a NIfTI

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Act 1 / 5 · the file

Just bytes

A NIfTI file is a 348-byte header followed by one long list of numbers. The header says how to read that list: how many voxels along each axis, how big each one is, and what type each number is.

sizeof_hdr	348
dim	[3, 96, 116, 96, 1, 1, 1, 1]
datatype	2 (uint8)
bitpix	8
pixdim	[1, 2.0, 2.0, 2.0, …] mm
vox_offset	352
sform_code	1 (scanner)
magic	"n+1\0"

Then, starting at byte 352, the data. Each cube is one value. The dim ones are zeros: empty space outside the head is stored too.

Act 2 / 5 · memory order

The fold

The list has no shape on its own. dim gives it one: the first 96 values fill a row along i, 116 rows fill a slice along j, and 96 slices stack along k.

n = i + 96·(j + 116·k)
0 = 0 + 96·(0 + 116·0)

Watch the write cursor drop each value into its cell. Tiny ghosts mark zeros on the current slice: most of the file is empty space.

progress 0%

write speed 0 / s

Act 3 / 5 · voxels

A brain of cubes

Each cube is one voxel: a 2 mm sample of tissue holding a single number. On a T1 image white matter is bright, gray matter is mid-gray, and CSF is dark. The threshold starts just above CSF so the folds show; drag it to 0 to wrap the brain in fluid.

explode 0

mode

color

threshold 0

cut-away off

hover any voxel to read its index and value

Act 4 / 5 · the affine

Index space → the scanner

An index says where a voxel sits in the array, not in the head. The sform affine is a 4×4 matrix mapping (i, j, k) to millimetres: it scales by voxel size, tilts with the slice angle, and moves the origin.

voxel indicesscanner mm

Colored axes are the array's i/j/k. Faint ones are the scanner's x (right), y (anterior), z (superior).

Act 5 / 5 · the 4th dimension

Time

A BOLD run is the same idea with one more axis: a coarser 4 mm volume every TR = 2 s, here 120 of them. Every voxel holds a timeseries. Warm voxels rise with the task: visual cortex in visual blocks, motor cortex in tapping blocks.

view

volume 0 / 120

activation threshold 0.9 %

stacked slice (k) 25

selected voxelvisual designmotor design

click a voxel to plot its timeseries

voxel

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Growing a brain…

Generating a simulated T1 volume and a 120-volume BOLD run, then uploading them to your GPU.