Before we start

From the scanner to our computer

Figure 1

T1w, T2w and FLAIR anatomical MRI images

Figure 2

BOLD functional MRI image

Figure 3

Functional MRI time series

Figure 4

Diffusion MRI images

Figure 5

Diffusion MRI tractogram

Figure 6

dicom-to-nifti

Anatomy of a NIfTI

Figure 1

t1_data contains 3 dimensions. You can think of the data as a 3D version of a picture (more accurately, a volume). NumPy array layouts

Figure 2

While typical 2D pictures are made out of squares called pixels, a 3D MR image is made up of 3D cubes called voxels. MRI slices

Figure 3

T1w image slices From left to right: sagittal, coronal and axial slices.

Figure 4

Coordinate systems

Data organization with BIDS

Exploring open MRI datasets

BIDS derivatives

Figure 1

BIDS App containerization