Update README.md

README.md

 # spinal_dmri_pipeline
 
-Scripts for processing spinal cord dMRI data.
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+Scripts for processing spinal cord dMRI data.
+
+# Content:
+
+- scripts
+  - `spinal_preproc.sh`
+  
+    - Runs Topup/Eddy and gets the data ready for model fitting.
+  
+  - `spinal_models.sh`
+ 
+    - Runs different flavours of DTI (standard, kurtosis, and free-water elimination). 
+    - Runs bedpostX
+    - Runs TDI
+
+# How to install
+
+```bash
+git clone git.fmrib.ox.ac.uk/saad/spinal_dmri_pipeline
+cd spinal_dmri_pipeline
+pip install
+```
+
+# How to run
+
+1. spinal_preproc.sh <dwi_file> <revPE_file> <output_dir>
+
+2. spinal_models.sh <output_dir>
+
+
+
+# Dependencies
+- FSL (6.0.5 or higher)
+- Spinal Cord Toolbox