From d243a05e261a5c93a7489f4ca41787456586c009 Mon Sep 17 00:00:00 2001
From: BKarat <64658250+Bradley-Karat@users.noreply.github.com>
Date: Fri, 14 Jul 2023 06:57:20 -0700
Subject: [PATCH] Update README.md

---
 README.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/README.md b/README.md
index 1ccd5cb..d9ed1d8 100644
--- a/README.md
+++ b/README.md
@@ -22,6 +22,16 @@ or
 poetry shell
 SANDI_python_toolbox
 ```
+Run either of these with the -h flag to get a detailed summary of the toolbox and its flags plus required arguments.
+## Example Toolbox Call
+For a dry-run:
+```
+poetry run SANDI_python_toolbox /path/to/bids/inputs /path/for/outputs participant --Delta 23.6 --Small_Delta 7 --cores all -np
+```
+To actually run the software:
+```
+poetry run SANDI_python_toolbox /path/to/bids/inputs /path/for/outputs participant --Delta 23.6 --Small_Delta 7 --cores all
+```
 ## Example File Struture
 ```
 └── bids
@@ -40,3 +50,4 @@ SANDI_python_toolbox
     │     ├── sub-02_dwi.nii.gz
     │     └── sub-02_noisemap.nii.gz
 ```
+Alternatively, the `--path-dwi` flag can be used to override BIDS by specifying absolute paths. For example: `--path-dwi /path/to/my_data/{subject}/dwi.nii.gz`. The other necessary files (.bval, .bvec, noisemap and brainmask) must be labelled in a similar fashion (i.e. all have the same prefix).