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I will need to add a new variable to the config file, and it is going to be the prfprepare/analysis-xx folder name, so that it know where to look for the data. For example:
in derivatives/prfanalyze y will create a folder called analysis-yy, and I will write the config file at this level. In the config file I will specify from where in prfprepare I want the data to be read, analysis-xx or whatever, and I will specify what kind of analyses I want to do, and I will have all of the supporting files for this project.
In the Docker, pass the input folder as read only. Remember to change the current behavior: input will be mapped to prfprepare/ and internally we know fromthe config file to read analysis-xx, the output will be mapped to prfanalyze/vista/analysis-yy...
If the config file has isPRFSynthData=False, then read the data from derivatives/prfprepare
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