Update README.md

Author: dadashkarimi

README.md

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 # Cross Atlas Remapping via Optimal Transport (CAROT)
 
 This is the repository for CAROT, ross Atlas Remapping via Optimal Transport. All the data including `mappings`, `intrinsic evluation`, and `downstream analysis` are in `data/` folder.
+
+
+## Creating mappings 
+The main code to create mappings, connectomes in a desired atlas, and testing is available in `hcp_atlas_to_atlas.py`.
+The following arguments are needed to call the script:
+
+1. `-s` or `--source`: source atlas
+2. `-t` or `--target`: target atlas
+3. `-c` or `--c`: cost matrix (euclidean or functional)
+4. `-task` or `--task`: task ("rest1","gambling","wm","motor","lang","social","relational","emotion")
+5. `-id` or `--id`: id rate (True or False)
+6. `-id_direction` or `--id_direction`: (ot-ot or orig-orig)
+7. `-intrinsic` or `--intrinsic`: parameter sensitiviy (True or False)
+8. `-simplex` or `--simplex`: (1: simplex ot, 2: average ot, 3: stacking ot, default is 2)
+9. `-num_iters` or `--num_iters`: number of iterations in test
+10. `-save_model` or `--save_model`: (True or False)
+
+
+```console
+javid@ycs:~$ python hcp_atlas_to_atlas.py -s brainnetome -t shen -task rest1 --save_model True -c euclidean
+```
+
+
+## Connectome Correlation and Downstream Analysis