Running a sample subject - McIntosh-Lab/tvb-ukbb GitHub Wiki

We've included a sample subject from the Amsterdam Open MRI Collection, a multi-modal MRI dataset that works with our pipeline. This subject will be used to demonstrate the processing and outputs of the pipeline.

We have also included outputs generated by our processing of the subject in case users would like to validate their outputs against ours. Outputs include the QC report using the Schaefer-Tian 420 parcellation,, the IDPs using the same parcellation, the MELODIC/FIX outputs, and the logs from the full pipeline.

Instructions

  1. cd into the tvb-ukbb repository and run git fetch. This will pull the amsterdam branch from the repository.

  2. Run git checkout amsterdam to enter the amsterdam branch. The subject's data is located in sample_subjects/amsterdam/sub-0001 within the tvb-ukbb directory. The raw data for the subject is located in sample_subjects/amsterdam/sub-0001/rawdata; the remaining directories are outputs generated by us. Copy the subject folder (containing only the rawdata subdirectory) to the location in which you wish to process the subject.

  3. Follow the instructions for Running on a HPC/non-HPC system or Running on Compute Canada.

  4. Allow the subject to run to completion. Feel free to validate your outputs against what we have provided in the repository.