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+# Installation 
+
+## Table of Contents 
+    
+- [Getting Started](#Getting-Started)
+- [Pre-trained Models](#Pre-trained-Models)
+- [Automated Scripts](#Automated-Scripts)
+  * [Segmentation](#Automated-Scripts)
+  * [Motion Estimation](#Motion-Estimation)
+  * [Strain Analysis](#Strain-Analysis)
+
+## Getting Started 
+
+Install the requirements: 
+
+- Linux or macOS
+- Python 3
+- CPU or NVIDIA GPU + CUDA CuDNN
+
+- Clone this repo:
+```bash
+git clone -b master --single-branch https://github.com/moralesq/DeepStrain.git
+cd DeepStrain
+```
+- Install TensorFlow and dependencies from https://www.tensorflow.org/install
+- Install python libraries   
+
+For pip users:
+```bash
+bash ./scripts/install_pip.sh
+```
+
+## Pre-trained Models
+
+- Download some test data in nifti format:
+```bash
+bash ./datasets/download_sample_dataset.sh
+```
+- Download the pre-trained models (i.e., carson and carmen):
+```bash
+bash ./pretrained_models/download_model.sh
+```
+
+## Automated Scripts
+
+### Segmentation
+
+- Generate segmentations with the model for 3D niftis:
+```bash
+bash ./scripts/test_segmentation.sh ./datasets/sample_nifti_3D NIFTI ./results/sample_nifti_3D
+```
+The test results will be saved to a nifti file here: `./results/sample_nifti_3D/`.
+
+- Generate segmentations with the model for 4D (3D+time) niftis:
+```bash
+bash ./scripts/test_segmentation.sh ./datasets/sample_nifti_4D NIFTI ./results/sample_nifti_3D
+```
+The test results will be saved to a nifti file here: `./results/sample_nifti_4D/`.
+
+### Motion Estimation
+
+- Generate motion estimates with the model for 4D (3D+time) niftis. Note that for motion estimation only 4D is supported:
+```bash
+bash ./scripts/test_motion.sh ./datasets/sample_nifti_4D NIFTI ./results/sample_nifti_4D
+```
+The test results will be saved to a h5 file here: `./results/sample_nifti_4D/`.
+
+- Generate both segmentation and motion estimates with the model for 4D (3D+time) niftis:
+```bash
+bash ./scripts/test_segmentation_motion.sh ./datasets/sample_nifti_4D NIFTI ./results/sample_nifti_4D
+```
+The test results will be saved to nifti and h5 files here: `./results/sample_nifti_4D/`.
+
+### Strain Analysis
+
+- After the segmentations and motion estimates have been generated, we can use both to calculate myocardial strain. Note that we're passing the output folder from the previous runs:
+```bash
+bash ./scripts/test_strain.sh ./results/sample_nifti_4D
+```
+The test results (4D radial and circumferential strain) will be saved to nifti files here: `./results/sample_nifti_4D/`.
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