From e6a47211410ed57705e2ec32adb397ac6663d061 Mon Sep 17 00:00:00 2001
From: Unique-Usman <usmanakinyemi202@gmail.com>
Date: Tue, 12 Mar 2024 16:27:57 +0530
Subject: [PATCH] Update the README file to include the information the
 sim_vim_sig.py and also how to run the script.

---
 phantoms/MR_XCAT_qMRI/README.md | 62 ++++++++++++++++++++++++++++++++-
 1 file changed, 61 insertions(+), 1 deletion(-)

diff --git a/phantoms/MR_XCAT_qMRI/README.md b/phantoms/MR_XCAT_qMRI/README.md
index f280597..3b95f52 100644
--- a/phantoms/MR_XCAT_qMRI/README.md
+++ b/phantoms/MR_XCAT_qMRI/README.md
@@ -1 +1,61 @@
-# MR_XCAT_qMRI
\ No newline at end of file
+# 4D IVIM Phantom Generator
+
+A command-line tool for generating a 4D IVIM (Intravoxel Incoherent Motion) phantom as a NIfTI file.
+
+## Usage
+
+```sh
+python sim_vim_sig.py  [-h] [-b BVALUE [BVALUE ...] | -f FILE] [-n NOISE] [-m] [-i]
+```
+
+## Arguments
+
+- `-b`, `--bvalue` : B values (list of numbers)
+- `-f`, `--bvalues-file` : JSON file containing the B values (default: b_values.json)
+- `-n`, `--noise` : Noise level (default: 0.0005)
+- `-m`, `--motion` : Enable motion flag (default: False)
+- `-i`, `--interleaved` : Enable interleaved flag (default: False)
+
+**Note:** Either provide `--bvalue` or `--bvalues-file`, not both.
+
+If neither `--bvalues-file` nor `--bvalue` is provided, the script will use the default `b_values.json` file.
+
+## Customizing B Values
+
+You can customize the B values by editing the `b_values.json` file. Here's an example of the default format:
+
+```json
+{
+    "original": [0.0, 1.0, 2.0, 5.0, 10.0, 20.0, 30.0, 50.0, 75.0, 100.0, 150.0, 250.0, 350.0, 400.0, 550.0, 700.0, 850.0, 1000.0],
+    "one": [0.0, 1.0, 2.0, 5.0, 10.0, 20.0, 30.0, 50.0, 75.0, 100.0, 150.0, 250.0, 350.0, 400.0, 550.0, 700.0, 850.0, 1000.0, 1100.0, 1200.0],
+    "two": [0.0, 1.0, 2.0, 5.0, 10.0, 20.0, 30.0, 50.0, 75.0, 100.0, 150.0, 250.0, 350.0, 400.0, 500.0, 700.0, 800.0, 1000.0, 1100.0, 1200.0],
+    "three": [0.0, 1.0, 2.0, 5.0, 10.0, 20.0, 30.0, 50.0, 75.0, 100.0, 150.0, 250.0, 350.0, 450.0, 550.0, 675.0, 800.0],
+    "four": [0.0, 1.0, 2.0, 5.0, 10.0, 20.0, 30.0, 50.0, 75.0, 100.0, 150.0, 250.0, 300.0, 400.0, 500.0, 600.0, 700.0, 800.0]
+}
+```
+
+You can add or remove values as needed for your simulation. Here are the effects of customizing the B values for each of the generic profiles (`generic.json`, `generic_one.json`, `generic_two.json`, `generic_three.json`, `generic_four.json`):
+
+The default `generic_<custom_name>.json` file can be found in the following location:
+
+```
+TF2.4_IVIM-MRI_CodeCollection/tests/IVIMmodels/unit_tests
+```
+
+## Running the Script
+
+To run the script, you can add the following line to your shell configuration file (e.g., `.bashrc` or `.zshrc`) to include the necessary directory in your `PYTHONPATH`:
+
+```sh
+export PYTHONPATH=$PYTHONPATH:~/TF2.4_IVIM-MRI_CodeCollection
+```
+
+Replace `~/TF2.4_IVIM-MRI_CodeCollection` with the actual path to the directory containing the script.
+
+## Example
+
+```sh
+python sim_ivim_sig.py -n 0.0001 -m
+```
+
+This command will generate a 4D IVIM phantom using B values from the default `b_values.json` file, with a noise level of 0.0001 and motion enabled.