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neuropoly / template

A framework for creating unbiased MRI templates of the spinal cord
MIT License
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Updated documentation for running the `template generation pipeline` in Alliance Canada #79

Closed rohanbanerjee closed 9 months ago

rohanbanerjee commented 10 months ago

Fixes #76, fixes #77

This README.md updates some missing steps for setting up and running the generate_template.py on Alliance Canada. Some specific details like setting up the nist_mni_pipelines inside the template folder, creation of virtual environment etc were missing.

To test this PR,

  1. Copy the data from duke/temp/rohan/bids_data to the Alliance Canada cluster following step 2.a.
  2. Follow the next steps in the step 2 to run the template generation pipeline.

Expected output

The pipeline would create a folder model_n_all inside the template folder. For each and every iteration of the template generation process, a folder would be created inside the model_n_all folder.