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Quality control, quantifying regional values, and querying of ANTs output. There are three main components to QuANTs.

• An R package that provides functions for obtaining summary values for images processed by the ANTs cortical thickness pipeline
• Rscripts used to generate .csv files that summarize measures using predefined anatonical labeling systems
• Some simple tools to help in performing QC

Here we will focus on 1, the R functions that may be used to access the data in a hopefully convenient way. For questions (at Penn) please post on the #quants channel at https://ftdc-picsl.slack.com

Rather than installing QuANTs on your own machine it may be easiest to use the R installed on the cluster:
export R_LIBS=""
export R_LIBS_USER=""
/data/grossman/pipedream2018/bin/R/R-3.4.3/bin/R
> library(QuANTs)

The workhouse of the package is the getQuants function. Follow the link to learn more about its basic use and links to helper functions that can make more complex tasks less complicated. The basic idea behind getQuants is that it allows the user to treat the output of the image processing pipeline as a database that one can query to obtain the data of interest. In other words, getQuants attempts to fulfill the following request: "For the data stored at this location, I would like to obtain this summary of this measure in this anatomy for these subjects whose data was acquired on these dates."