remake data organization

[brainspinner]

setup with instructions so that json is inside not_pushed, and get better instructions

[brainspinner]

Now needs testing and discussion with scientists. On branch drcandacemakedamoore/into_test_data

[MDijsselhof]

ASL-BIDS folder structure is as follows:

• studyfolder
  • sourcedata (DICOMS)
  • rawdata (.NII)
  • derivatives
    • ExploreASL (example)
    • cvage
      • input_folder
      • output_folder
      • Etc.
  • config.json

So in summary, all data to be processed should be copied from the rawdata into the derivatives folder and corresponding image processing/analysis pipeline which in our case would be 'cvage'

[brainspinner]

So to summarize, the data will be in a seperate folder as per scientist request, but the json needs to create the above structure automatically.,.

[MDijsselhof]

To summarise the meeting on monday 25th: We will assume the user will provide ASL data per (ASL)-BIDS standard. This means the user will have created the files described above, and cvage will use a config.json file located in the main study folder (see the edited comment above). cvage will copy all imaging data from rawdata into derivatives/cvage and start processing there.