diff --git a/book.toml b/book.toml index d34134a..7ceeba1 100644 --- a/book.toml +++ b/book.toml @@ -3,3 +3,6 @@ authors = [] language = "en" multilingual = false src = "src" +title = "Styx Book" + +[preprocessor.alerts] \ No newline at end of file diff --git a/src/2_getting_started.md b/src/2_getting_started.md index 69a5d54..56e219d 100644 --- a/src/2_getting_started.md +++ b/src/2_getting_started.md @@ -1 +1,42 @@ # Getting started + +> [!NOTE] +> This book uses Styx wrappers from the NiWrap package, but any Styx wrapper will work the same way. + +To get started install the [NiWrap](https://github.com/childmindresearch/niwrap/tree/main) Python package: + +```sh +pip install -e "git+https://github.com/childmindresearch/niwrap.git/#egg=niwrap&subdirectory=python" +``` + +From there on running commands will be as easy as: + +```Python +from niwrap import fsl + +bet_output = fsl.bet( + infile="my_file.nii.gz", + binary_mask=True, +) +``` + +This runs the command + +```sh +bet my_file.nii.gz -m +``` + +and stores all the output files for easy access in `bet_output`. + +These can then be used as an input to another Styx wrapper or with any other Python package like nilearn: + +```Python +from nilearn.plotting import plot_anat + +plot_anat(bet_output.outfile) +``` + +> [!TIP] +> Styx includes detailed documentation about every command, argument, and output file. You should be able to just hover over any of them in your editor to view its documentation. + +The next chapter will explain how to use _Runners_ to control how the commands get executed and intermediate files get stored. \ No newline at end of file diff --git a/src/2a_installation.md b/src/2a_installation.md deleted file mode 100644 index 25267fe..0000000 --- a/src/2a_installation.md +++ /dev/null @@ -1 +0,0 @@ -# Installation diff --git a/src/SUMMARY.md b/src/SUMMARY.md index 6d0d416..bd01340 100644 --- a/src/SUMMARY.md +++ b/src/SUMMARY.md @@ -2,7 +2,6 @@ - [The Styx Book](./1_welcome.md) - [Getting started](./2_getting_started.md) - - [Installation](./2a_installation.md) - [Runners](./2b_runners.md) - [Tips & best practices](./2c_tips_best_practices.md) - [Contributing to NiWrap](./2d_contributing_to_niwrap.md)