Metric Correlation Matrix Cifti

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  1. Update to read and write Cifti files using the new Cifti reader
  2. Update help to document that Cifti files are allowed (using the help below).
  3. Fix bug that causes data corruption of output metric data. (Matt, please add more detail about how to reproduce this bug, preferably below).

Below is the proposed help for the update version of METRIC CORRELATION MATRIX:

     caret_command -metric-correlation-matrix  
        Compute a correlation matrix using the input metric file.
        The input metric file can be in either Gifti or Cifti format.
        Both input and output files need to be of the same type.
        Each row (node) in the metric file is correlated with all
        other rows in the metric file.  Each column in the metric
        file represents an "observation" at each node.  
        The number of rows and columns are the same in the output
        metric file and are equal to the number of rows from the 
        input metric file.  The values in the output metric file 
        form a symmetric matrix with each element containing 
        a correlation coefficient for the data of two nodes where
        the node numbers are the row and column indices.
        An example input metric file is one in which each row
        represents nodes and each column represents timepoints. 
        The output metric file contains correlation coefficients
        that measure the similarity of the timepoints from all
        nodes to all nodes.
        If "-apply-fisher-z-transform" options is specified a
        is applied to the correlation values.
        If the "-parallel" option is specified, the algorithm
        will run its operations with multiple threads to reduce
        execution time.
        Run "caret_command -help-global-options"
           for parameters available to all commands.
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