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Parsing and Extract Metadata of T1w images in HCP dataset, and Uploading the Images with Metadata into Bisque

Add annotation of T1w images in HCP dataset by parsing its absolute path to build metadata, and then upload the images with their metadata into Bisque.

Using Steps

  1. Log in to your Brain server account
ssh [email protected]
  1. clone the repositroy to your account
  2. install the require libraries
pip install pandas  
pip install re
pip install uuid
pip install bqapi
pip install lxml
  1. edit #username# and #password# in UpLoadHCPfiles.py at line #11
bq_session = BQSession().init_local('#username#', '#password#', bisque_root=BISQUE_ROOT_URL, create_mex=True)
  1. Run the code
python UpLoadHCPfiles.py

Explaination

line#8: this is the declaration of the path of .csv file

CSV_PATH = './HCPMetadata.csv'

line#9: this is the path of what directory you want to upload and here is the whole HCP dataset directory path in Brain server

BASE_FILE_PATH = '/cluster/brain/connectome_disks'

line#10: here is the Bisque root url which will add to the url of metadata and send to Bisque

BISQUE_ROOT_URL = 'https://bisque.ece.ucsb.edu'

Authors

Akshay Heda, Suhail Chakravarty, Calvin Jenkins, Ziming Qi