Purpose: Compute the relevant statistics for a single QA data set, store them in a common directory, and maintain a text file of cumulative statistics.

Usage: mrqa directory_name

Inputs: path to the top level of a directory tree containing EPI data and/or images and structural images.

Outputs:

1. A directory named ${MR_QC_OUTPUT_PATH}/yyyymmmdd containing the following items:
   1. Images of the mean EPI deviation, Mean spin-echo deviation, the "worst" image frame (the one with the largest nonuniformity), the EPI mean and standard deviation, and the signal-to-flucutuation_noise (SFNR) ratio. All images are in analyze format.
   2. Text file containing the mean ghost as a function of frame number.
2. An entry in the file ${MR_QC_OUTPUT_PATH}/cumulative_qc_statistics.txt containing the scalar statistics computed for this date.

Dates: All dates are determined by reading the date stored in the P-file used to reconstruct the EPI images. Plots vs date use the integer number of days since the first dataset was acquired.

Environment Variables: MR_QC_OUTPUT_PATH specifies the directory where results should be stored. This variable defaults to /study/MR3T_QC.

Method: The program searches paths below the directory specified by the program argument to find all EPI files and structural images that can be used in the calculations. The EPI images are reconstructed with epirecon if this hasn't already been done.