updating examples

README.md

@@ -39,10 +39,23 @@ The scattered nature of health data, along with the lack of standardization and
 
 ## Installation
 
-By pulling the latest version from GitHub. Please note that your Python installation should be 3.6 or later. 
+1. To perfome the **installation** you should clone the latest version from GitHub. Please note that your Python installation should be 3.6 or later. 
 ```
 git clone https://github.com/kildealab/mCODE-MOSAICO
 ```
+2.  To install the **dependecies**
+```
+cd mCODE-MOSAICO
+pip install -r requirements.txt
+```
+
+3. To **import** the package in Jupyter Notebook or Python3 file
+
+```
+import sys
+sys.path.append('/path/to/the/folder/mCODE-MOSAICO/utils')
+```
+
 ## Usage and Examples
 <p align="center">
 <img src="/diagrams/mCODE_Ext_diagram.png" width="1000">
@@ -91,6 +104,48 @@ git clone https://github.com/kildealab/mCODE-MOSAICO
 |   └── ...
 </pre>
 
+### Sort and Save Images 
+
+### Save mCODE attributes
+
+### Features and Factors Extraction
+
+##### (1) Radiomics
+
+To extract **only** the **radiomics** for a single patient and a single ROI 
+```
+python extract_only_radiomics patient ROI
+```
+
+To extract **only** the **radiomics** for *all* the patient and *all* the available ROIs
+```
+python extract_only_radiomcis all all
+```
+
+##### (2) Dosiomics 
+
+To extract **only** the **dosiomics** for a single patient and a single ROI 
+```
+python extract_only_dosiomics patient ROI
+```
+
+To extract **only** the **dosiomics** for *all* the patient and *all* the available ROIs
+```
+python extract_only_dosiomics all all
+```
+
+##### (3) Dosimetric (DVH factors)
+To extract **only** the **dosimetric or dvh factors** for a single patient and a single ROI 
+```
+python extract_only_dvh_factors patient ROI
+```
+
+To extract **only** the **dosimetric or dvh factors** for *all* the patient and *all* the available ROIs
+```
+python extract_only_dvh_factors all all
+```
+### Full pipeline
+
 ## License 
 This project is provided under the GNU General Public License version 3 (GPLv3) to preserve open-source access to any derivative works. See the LICENSE file for more information.
 ## References