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In the docs/tutorials, code examples are written as follows:

$ miracl -h

Code blocks look like this:

usage: miracl [-h] {connect,conv,flow,lbls,reg,seg,sta,stats,utils} ...

positional arguments:
  {connect,conv,flow,lbls,reg,seg,sta,stats,utils}
    connect             connectivity functions
    conv                conversion functions
    flow                workflows to run
    lbls                label manipulation functions
    reg                 registration functions
    seg                 segmentation functions
    sta                 structure tensor analysis functions
    stats               statistical functions
    utils               utility functions

optional arguments:
  -h, --help            show this help message and exit

Inline code is marked as: $ miracl -h

Admonitions are displayed as colored text boxes. This is an example of what a ‘tip’ admonition would look like:

Tip

The above -h flag can be used with each of MIRACL’s modules/functions

We use brackets to denote text as follows:

• {}: Used for variabels.

  • Example: niftis/downsample{factor}x.nii.gz

• <>: Used for placeholder text in examples that you need to replace with your own information.

  • Example: $ ssh <username>@cedar.computecanada.ca

• [ ]: Placeholders for flag arguments used in command-line scripting.

  • Example: $ miracl flow sta -f [ Tiff folder ] -o [ output nifti ]

• []: Denotes flags in the command-line help menus.

  • Example: $ miracl [-h]

Files and directories (or generally paths) are denoted like this: example_dir/example_file.nii.gz

Names of exectutable programs are marked as follows: MIRACL

Lastly, links are highlighted in blue (purple when clicked): link to MIRACL’s README