BXH/XCEDE Tools manual

Usage:
  afni2bxh [opts] afnifile.HEAD output.bxh

This program creates an XML wrapper for AFNI images.

  --inputsfromfile <str>
  --inputsfromfile=<str>
        Read list of input files from this file.
  --version
        Print version string and exit.
  --hintsizex <size_t>
  --hintsizex=<size_t>
  --hintsizey <size_t>
  --hintsizey=<size_t>
  --hintsizez <size_t>
  --hintsizez=<size_t>
  --hintsizet <size_t>
  --hintsizet=<size_t>
  --hintoriginx <double>
  --hintoriginx=<double>
  --hintoriginy <double>
  --hintoriginy=<double>
  --hintoriginz <double>
  --hintoriginz=<double>
  --hintorigint <double>
  --hintorigint=<double>
  --hintspacingx <double>
  --hintspacingx=<double>
  --hintspacingy <double>
  --hintspacingy=<double>
  --hintspacingz <double>
  --hintspacingz=<double>
  --hintspacingt <double>
  --hintspacingt=<double>
  --hintgapx <double>
  --hintgapx=<double>
  --hintgapy <double>
  --hintgapy=<double>
  --hintgapz <double>
  --hintgapz=<double>
  --hintgapt <double>
  --hintgapt=<double>
        These options will provide a hint to the program of the 'size',
        'origin', 'spacing', or 'gap' of the specified dimension.  Some image
        types will not use all these values.  In particular, sizex and sizey
        are assumed correct in most image headers, but they, as well as sizez
        and sizet options may be useful with image type 'pfile'.  Origin and
        spacing hints will be used by most image types.  
  --forceorientation <str>
  --forceorientation=<str>
        This option will force the labeled orientation of the image to match
        the given three letter orientation code.  Each letter must come from
        the following groups in any order: R(ight) or L(eft); A(nterior) or
        P(osterior); S(uperior) or I(nferior).  Only one letter from each group
        is allowed.
  --xcede
        Write XCEDE-style XML files.
  --xcede2
        Write XCEDE 2-style XML files.

Usage:
  analyze2bxh [opts] [analyzefiles...] output.bxh

This program creates an XML wrapper for Analyze7.5/SPM/NIfTI-1 images.

  --orientation <str>
  --orientation=<str>
        Orientation of image, letters indication which way theX, Y, and Z
        dimensions (in that order) are pointing (e.g. LPS, IRP).  Default is
        RAS (i.e. orientation used by SPM), or that specified in accompanying
        SPM .mat files.  This option overrides all info in SPM .mat files
        and/or the Analyze 'orient' field (if --strictanalyze is specified).
        Equivalent to (and overrides) --forceorientation.
  --strictanalyze
        Don't use SPM .mat files and use Analyze convention for orientation.
        The 'orient' field in the analyze header is parsed, and the default
        case (i.e. it is zero) means 'LAS'.
  --avwbyteorder <str>
  --avwbyteorder=<str>
        Specify byte order for AVW files (which don't store this info). This
        field should be 'l' for little-endian or 'b' for big-endian.
  --inputsfromfile <str>
  --inputsfromfile=<str>
        Read list of input files from this file.
  --version
        Print version string and exit.
  --hintsizex <size_t>
  --hintsizex=<size_t>
  --hintsizey <size_t>
  --hintsizey=<size_t>
  --hintsizez <size_t>
  --hintsizez=<size_t>
  --hintsizet <size_t>
  --hintsizet=<size_t>
  --hintoriginx <double>
  --hintoriginx=<double>
  --hintoriginy <double>
  --hintoriginy=<double>
  --hintoriginz <double>
  --hintoriginz=<double>
  --hintorigint <double>
  --hintorigint=<double>
  --hintspacingx <double>
  --hintspacingx=<double>
  --hintspacingy <double>
  --hintspacingy=<double>
  --hintspacingz <double>
  --hintspacingz=<double>
  --hintspacingt <double>
  --hintspacingt=<double>
  --hintgapx <double>
  --hintgapx=<double>
  --hintgapy <double>
  --hintgapy=<double>
  --hintgapz <double>
  --hintgapz=<double>
  --hintgapt <double>
  --hintgapt=<double>
        These options will provide a hint to the program of the 'size',
        'origin', 'spacing', or 'gap' of the specified dimension.  Some image
        types will not use all these values.  In particular, sizex and sizey
        are assumed correct in most image headers, but they, as well as sizez
        and sizet options may be useful with image type 'pfile'.  Origin and
        spacing hints will be used by most image types.  
  --forceorientation <str>
  --forceorientation=<str>
        This option will force the labeled orientation of the image to match
        the given three letter orientation code.  Each letter must come from
        the following groups in any order: R(ight) or L(eft); A(nterior) or
        P(osterior); S(uperior) or I(nferior).  Only one letter from each group
        is allowed.
  --xcede
        Write XCEDE-style XML files.
  --xcede2
        Write XCEDE 2-style XML files.

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Usage:
  bxh2analyze [opts] input.bxh outputprefix

  xcede2analyze [opts] input.bxh outputprefix

Both programs create Analyze 7.5, SPM, or NIfTI-1 images from BXH- or XCEDE-
wrapped images (both programs support both formats).  NOTE: XCEDE is only
supported if this program was compiled with XSLT support (which in this case,
it has; congratulations!).

  --version
        Print version string and exit.
  --overwrite
        Overwrite files if they exist.
  --bxh
        This option forces output XML file to be BXH (this option is ignored by
        [and is the default behavior of] bxh2analyze)
  --xcede
        This option forces output XML file to be XCEDE (this option is ignored
        by [and is the default behavior of] xcede2analyze)
  --xcede2
        This option forces output XML file to be XCEDE2.
  -b
        This option suppresses the writing of a BXH/XCEDE header for every
        Analyze header and image file. 
  -s
        This option suppresses the writing of an SPM .mat file for every
        Analyze header and image file. 
  -i
        This option suppresses the writing of the image (.img) files.
  -h
        This option suppresses the writing of the Analyze header (.hdr) files.
  -B
        If writing BXH/XCEDE headers, instead of writing one header, this
        option forces the writing of several BXH/XCEDE headers, one per Analyze
        header and image file. 
  -v
        This option suppresses the splitting a time series into separate
        volumes.  If not specified, then each image file will contain the data
        for one volume.  If specified, then each time series will be output as
        one large file.
  --niftihdr
        Generate NIfTI-1 format header (default is to attempt to generate a
        maximally compatible header).
  --nii
        Use NIfTI-1 one-file convention (header and data in same file).  Output
        image files will have the .nii extension.  This option automatically
        turns on --niftihdr and -v.
  --niigz
        Same as (and overrides) --nii, but the output will be compressed and
        will have the .nii.gz extension.  
  --spmhdr
        Assume header will only be read by SPM, using SPM-specific values when
        possible (default is to attempt to generate a maximally compatible
        header).
  --analyzehdr
        Generate "pure" Analyze 7.5 header, whatever that means.  (default is
        to attempt to generate a maximally compatible header).
  --preferanalyzetypes
        Prefer the use of only Analyze 7.5 pixel types if we are writing SPM or
        NIfTI headers; non-Analyze 7.5 pixel types will be used if
        overflow/underflow is detected.  This option requires either the
        --spmhdr or --niftihdr options.
  --analyzetypes
        Force the use of only Analyze 7.5 pixel types, even if we are writing
        SPM or NIfTI headers.  If necessary, this will cause conversion to a
        data type with higher range.
  --nosform
        For NIfTI headers, do not write orientation information into the sform
        fields.  Default is to write both qform and sform.
  --spatialunits <str>
  --spatialunits=<str>
        Force spatial units to a given value.  Must be 'm', 'mm', or 'um'.
        Output metadata will not be converted if this does not correctly
        represent the input metadata.
  --temporalunits <str>
  --temporalunits=<str>
        Force temporal units to a given value.  Must be 's', 'ms', or 'us'.
        Output metadata will not be converted if this does not correctly
        represent the input metadata.
  --zeroorigin
        Force the origin fields in the output images to be [0,0,0] (this is
        useful if your analysis software uses 0,0,0 to mean 'unspecified', and
        you don't want to specify the origin).

Usage:
  bxh2pgm input.bxh output.pgm

This program converts images wrapped with a BXH or XCEDE header into PGM
format.  3-D or higher dimensionality images are represented as a sequence of
2-D images.

  --version
        Print version string and exit.
  --colorbar <str>
  --colorbar=<str>
        Write a horizontal colormap 'bar' to this PGM file.
  --colorbarorient <str>
  --colorbarorient=<str>
        Orientation of colorbar, either 'horizontal' (default) or 'vertical'.
  --barwidth <uint>
  --barwidth=<uint>
        Width (in pixels) of colormap 'bar' (default 16).
  --barlength <uint>
  --barlength=<uint>
        Length (in pixels) of colormap 'bar' (default 256).
  --maxval <double>
  --maxval=<double>
        By default, if the input element type is floating-point or if the
        maximum input value is greater than 65535, the maximum value in the
        input will be mapped to 65535 (the highest possible PGM value) in the
        output PGM image.  --maxval specifies an alternative maximum input
        value.  Input values greater than this will be clipped.
  --minval <double>
  --minval=<double>
        By default, the minimum value in the input will be mapped to 0 (the
        lowest possible PGM value) in the output PGM image.  --minval specifies
        an alternative minimum input value.  Input values smaller than this
        will be clipped.
  --dimorder <str>
  --dimorder=<str>
        Specify dimension order as a comma-separated list of dimension names.
  --timeselect <str>
  --timeselect=<str>
        Comma-separated list of timepoints to use (first timepoint is 0).  Any
        timepoint can be a contiguous range, specified as two numbers separated
        by a colon, i.e. 'START:END'.  An empty END implies the last timepoint.
        The default step of 1 (one) in ranges can be changed using
        'START:STEP:END', which is equivalent to
        'START,START+STEP,START+(2*STEP),...,END'.
  --xselect <str>
  --xselect=<str>
        Just like timeselect, but for the 'x' dimension.
  --yselect <str>
  --yselect=<str>
        Just like timeselect, but for the 'y' dimension.
  --zselect <str>
  --zselect=<str>
        Just like timeselect, but for the 'z' dimension.

Usage:
  bxh2ppm input.bxh output.ppm

This program converts images wrapped with a BXH or XCEDE header into PPM
format.  3-D or higher dimensionality images are represented as a sequence of
2-D images.

  --version
        Print version string and exit.
  --colorbar <str>
  --colorbar=<str>
        Write a colormap 'bar' to this PPM file.
  --nobracket
        If --colorbar specified, then --nobracket disables the 'bracket' in the
        colorbar that shows the color range displayed by this image.
  --colorbarorient <str>
  --colorbarorient=<str>
        Orientation of colorbar, either 'horizontal' (default) or 'vertical'.
  --barwidth <uint>
  --barwidth=<uint>
        Width (in pixels) of colormap 'bar' (default 16).
  --barlength <uint>
  --barlength=<uint>
        Length (in pixels) of colormap 'bar' (default 256).
  --maxval <double>
  --maxval=<double>
        By default, if the input element type is floating-point or if the
        maximum input value is greater than 65535, the maximum value in the
        input will be mapped to the color corresponding to the highest value in
        the output PPM image.  --maxval specifies an alternative maximum input
        value.  Input values greater than this will be clipped.
  --minval <double>
  --minval=<double>
        By default, the minimum value in the input will be mapped to the color
        corresponding to the lowest value in the output PPM image.  --minval
        specifies an alternative minimum input value.  Input values smaller
        than this will be clipped.
  --colormap <str>
  --colormap=<str>
        Use this colormap for converting input values to colors.  Valid
        colormaps are 'hot', 'bluered', 'grayhot', and 'gray' (default).
  --dimorder <str>
  --dimorder=<str>
        Specify dimension order as a comma-separated list of dimension names.
  --timeselect <str>
  --timeselect=<str>
        Comma-separated list of timepoints to use (first timepoint is 0).  Any
        timepoint can be a contiguous range, specified as two numbers separated
        by a colon, i.e. 'START:END'.  An empty END implies the last timepoint.
        The default step of 1 (one) in ranges can be changed using
        'START:STEP:END', which is equivalent to
        'START,START+STEP,START+(2*STEP),...,END'.
  --xselect <str>
  --xselect=<str>
        Just like timeselect, but for the 'x' dimension.
  --yselect <str>
  --yselect=<str>
        Just like timeselect, but for the 'y' dimension.
  --zselect <str>
  --zselect=<str>
        Just like timeselect, but for the 'z' dimension.

Usage:
  bxh_brainmask [opts] inputfile outputfile

This program will attempt to create a simple (thresholded) brain mask given a
BXH- or XCEDE-wrapped input image.  Output is also a BXH- or XCEDE-wrapped
input image.  Calculation of the threshold is modified using various options.

  --version
        Print version string and exit.
  --timeselect <str>
  --timeselect=<str>
        Comma-separated list of timepoints to use (first timepoint is 0).  Any
        timepoint can be a contiguous range, specified as two numbers separated
        by a colon, i.e. 'START:END'.  An empty END implies the last timepoint.
        The default step of 1 (one) in ranges can be changed using
        'START:STEP:END', which is equivalent to
        'START,START+STEP,START+(2*STEP),...,END'.  Default is all timepoints
        (:).
  --xselect <str>
  --xselect=<str>
        Just like timeselect, but for the 'x' dimension.
  --yselect <str>
  --yselect=<str>
        Just like timeselect, but for the 'y' dimension.
  --zselect <str>
  --zselect=<str>
        Just like timeselect, but for the 'z' dimension.
  --overwrite
        Overwrite existing output files (otherwise error and exit). 
  --method <str>
  --method=<str>
        Method to use for creating the brain mask.
        'threshold' marks those voxels whose mean value over time are not less
        than a given threshold (provided by --filterthresh).
        'rank' chooses the largest threshold that allows at least the n
        highest-valued voxels (as determined by the voxel's mean value over
        time) where n is specified by --filterrank.
        'localmin' fits a nth-order polynomial (order optionally specified by
        --filterorder) to an intensity histogram of the minimum value of each
        voxel over time, and chooses the first local minimum (disregarding the
        first histogram bucket) as the threshold.  This method assumes the data
        follows an intensity distribution with at least two "humps", the first
        (lower) of which reflects noise.
        Default is 'rank'.
  --filterorder <uint>
  --filterorder=<uint>
        Order of the polynomial used for --method localmin.  Default is 5.
  --filterthresh <str>
  --filterthresh=<str>
        Threshold used for --method threshold.  If value ends with the percent
        sign (%), then this is taken as a percent of maximum intensity.
        Default is '50%'.
  --filterrank <str>
  --filterrank=<str>
        Threshold used for --method rank.  If value ends with the percent sign
        (%), then this is taken as a percent of the number of total voxels.
        Default is '20%'.
  --debug
        Print out debugging messages.

Usage:
  bxh_correlate [opts] --template T1,T2,T3... inputxmlfile out_rfile
[out_tfile]

This program correlates the time series of each voxel in a 4-D time series of
volumes (inputxmlfile) with a given "template" vector (specified with
--template option).  Output (in out_rfile) is a 3-D data set storing the
correlation coefficient (r).  The optional third argument (out_tfile) is where
to write the 3-D data set storing the corresponding t-statistic (derived from
r).

  --version
        Print version string and exit.
  --optsfromfile <str>
  --optsfromfile=<str>
        Program options (i.e. those starting with '--') will come from this
        file.  If this option is specified, then the options in the file will
        be applied after all command-line options.  The options (and their
        arguments) should be specified one per line, with the leading '--'
        omitted.
  --overwrite
        Overwrite existing output files (otherwise error and exit). 
  --timeselect <str>
  --timeselect=<str>
        Comma-separated list of timepoints to use (first timepoint is 0).  Any
        timepoint can be a contiguous range, specified as two numbers separated
        by a colon, i.e. 'START:END'.  An empty END implies the last timepoint.
        The default step of 1 (one) in ranges can be changed using
        'START:STEP:END', which is equivalent to
        'START,START+STEP,START+(2*STEP),...,END'.  Default is all timepoints
        (:).
  --xselect <str>
  --xselect=<str>
        Just like timeselect, but for the 'x' dimension.
  --yselect <str>
  --yselect=<str>
        Just like timeselect, but for the 'y' dimension.
  --zselect <str>
  --zselect=<str>
        Just like timeselect, but for the 'z' dimension.
  --template <str>
  --template=<str>
        A comma-separated list of numbers making up the template vector to
        correlate with the data.  This option or --templatevoxel is required.
  --templatevoxel <str>
  --templatevoxel=<str>
        A comma-separated x,y,z coordinate (indices start at 0) indicating
        which voxel in the dataset to which to do the correlation.  The value
        at that voxel in the output will be 1.0.  This option or --template is
        required.
  --maskfile <str>
  --maskfile=<str>
        Use this 3-D mask (should be an XML file) before doing calculations.

Usage:
  bxh_epochavg [opts] outputprefix imgfile1 eventfile1[,eventfile1b,...]
[imgfile2 eventfile2[,eventfile2b,...] ...]

This program "queries" a 4-D data set (with corresponding event lists) and
produces averages of all time courses surrounding each event that match the
query.  Multiple independent queries may be specified, and the width and
position and duration of each time course relative to the event is also
user-specified.  Multiple event files corresponding to the same image data can
be specified separated by commas (the filenames/paths themselves are therefore
prohibited from containing commas).

  --version
        Print version string and exit.
  --optsfromfile <str>
  --optsfromfile=<str>
        Program options (i.e. those starting with '--') will come from this
        file.  If this option is specified, then the options in the file will
        be applied after all command-line options.  The options (and their
        arguments) should be specified one per line, with the leading '--'
        omitted.
  --overwrite
        Overwrite existing output files (otherwise error and exit). 
  --maskfile <str>
  --maskfile=<str>
        Use this 3-D mask (should be an XML file) before doing calculations.
  --querylanguage <str>
  --querylanguage=<str>
        The language used for all queries.  Valid values are 'XPath' and
        'event'.  Case is irrelevant.  Default is 'XPath'.
  --query <str>
  --query=<str>
        A query string as an XPath boolean expression.  Will be applied as a
        predicate filter to each event.  Each event node may or may not have
        onset, duration, type, and value elements (as well as others).
        Examples:
          --query "value[@name='color']='red'"
          --query "value[@name='color']='red' or value[@name='color']='blue'"
          --query "(value[@name='color']='red' or value[@name='color']='blue')
        and not value[@name='field']='upper' and onset>12000"
        Note that some characters in queries may need to be protected from the
        shell with quotes (as in the above examples).  Separate instances of
        the --query option will result in independent queries, with separate
        outputs.  Empty queries match all events.  NOTE: At least one query
        must be specified!
  --queryfilter <str>
  --queryfilter=<str>
        If this option is specified, it is an XPath query (like --query) that
        is applied to a list of pseudo-events, each pseudo-event corresponding
        to an event matching the original query.  Each pseudo-event is a
        merging of all events that are simultaneously in effect at the time of
        the onset of the real event.  If this query matches the pseudo-event,
        the real event passes through the filter.  The n-th instance of this
        option corresponds to the n-th specified query.  If any --queryfilter
        options are specified, there should be exactly one --queryfilter per
        --query.Empty or missing filter queries match everything.
  --queryepochexclude <str>
  --queryepochexclude=<str>
        Like --query, --queryepochexclude specifies an XPath-based event query.
        However, any epoch that includes an event that matches this query will
        be excluded from the analysis.  The epoch surrounding an event is
        specified using --ptsbefore and --ptsafter (or --secsbefore and
        --secsafter).  The n-th instance of this option corresponds to the n-th
        specified query.  If any --queryepochexclude options are specified,
        there should be exactly one --queryepochexclude per --query.Empty or
        missing epoch exclusion queries exclude nothing.
  --querylabel <str>
  --querylabel=<str>
        A textual label for the corresponding query.  The first instance of
        this option corresponds to the first specified query.  There should be
        at most one --querylabel per --query.  Default label is the query
        number.
  --ptsbefore <int>
  --ptsbefore=<int>
        How many time points before the event to include in analysis.  This
        option (or --secsbefore) is required.
  --ptsafter <int>
  --ptsafter=<int>
        How many time points after the event to include in analysis.  This
        option (or --secsafter) is required.
  --secsbefore <double>
  --secsbefore=<double>
        How many seconds before the event to include in analysis.  This option
        (or --ptsbefore) is required.
  --secsafter <double>
  --secsafter=<double>
        How many seconds after the event to include in analysis.  This option
        (or --ptsafter) is required.
  --basestartoffset <int>
  --basestartoffset=<int>
        Where to start calculating mean baseline, in number of timepoints (TRs)
        relative to event time.  A negative number refers to a timepoint before
        the event, 0 is at the time of the event, and a positive number is
        after the event.  Default is 0.
  --baseendoffset <int>
  --baseendoffset=<int>
        Where to end calculating mean baseline, in number of timepoints (TRs)
        relative to event time.  A negative number refers to a timepoint before
        the event, 0 is at the time of the event, and a positive number is
        after the event.  Default is 0.
  --startpt <uint>
  --startpt=<uint>
        This number of time points at the start of the data will be ignored.
        Default is 0.
  --endpt <uint>
  --endpt=<uint>
        Time points after this point will be ignored.  Default is last
        timepoint.
  --forcetr <double>
  --forcetr=<double>
        If specified, this value (in seconds) will replace the TR specified in
        the input image file, if any.
  --nointerp
        If specified, no interpolation will be done -- events will be assumed
        to occur at the closest TR/image acquisition time.
  --scalebl
        If specified, values in each epoch are additionally scaled by dividing
        by (after subtracting) the baseline.  This affects the 'avg' and 'std'
        output images.  Percent signal-change images are not written.  WARNING:
        Know what you are doing before using this option.
  --extracttrials
        If this option is specified, the program will write out epochs for
        *all* extracted trials to a file PREFIX_QUERY_trials.bxh.  This file
        will be a 5-D image file where the 4th dimension goes across time
        points within an epoch, and the 5th dimension represents the global
        trial number.
  --trialsummary <str>
  --trialsummary=<str>
        This option enables the creation of "summaries" of trials before
        averaging, where summaries are new trials where each point is an
        average of some number of timepoints in the original trial.  The string
        argument is of the form "QUERY-PTS", where QUERY is a query label, and
        PTS is a plus('+')-separated list of "index groups", an "index group"
        is a comma-separated list of indices or ranges (which are two indices
        separated by a colon).  For example "red-0" will create a summary
        trials containing only the first point in each trial that matches the
        "red" query, and "red-0:3+4:7+8:11" or "red-0,1,2,3+4,5,6,7+8,9,10,11"
        (both are equivalent) will average together the 12 timepoints of each
        "red" trial in groups of 4.  The outputs will be similar to other
        outputs but will look like PREFIX_QUERY_summary_PTS_avg.bxh etc., but
        with the colons (':') replaced with dashes ('-') due to problems some
        file systems have with colons.  Note that timepoints are indexed from
        0.  This option may be specified more than once.
  --trialmax
        This is an EXPERIMENTAL option.  If specified, a 'seed' timepoint and
        voxel is found within the optional ROI specified by --trialmaxroi.  The
        seed timepoint is defined as the timepoint within the epoch average
        that has the highest mean intensity.  The seed voxel is then defined as
        the voxel with the highest value within the seed timepoint.  Then, for
        each voxel, a 'trial sequence' is constructed containing the value of
        that voxel at the seed timepoint within each individual epoch (before
        averaging).  The output is a 4-D series of volumes (one for each trial)
        named PREFIX_QUERY_trialmax.bxh that contains the volumes at the seed
        timepoint in each trial.  The seed voxel coordinates are written to
        PREFIX_QUERY_trialmaxseed.txt.
  --trialmaxroi <str>
  --trialmaxroi=<str>
        The ROI used by --trialmax.
  --trialmaxseed <str>
  --trialmaxseed=<str>
        This specifies an explicit comma-separated coordinate X,Y,Z,T for the
        seed for --trialmax, to be applied to ALL queries.  The T coordinate
        must be in the range [0,s-1] where s is the number of time points in
        the epoch.  Note that timepoints are indexed from 0.
  --extracttimingonly
        If specified, only the PREFIX_LABEL_timing.txt files will be written.
  --memorylimit <double>
  --memorylimit=<double>
        This specifies the number of megabytes of the input data to read at a
        time.  Default is to read the entire data at once.  If you are running
        out of memory due to high-resolution data, or large numbers of
        timepoints, this is one way to reduce memory usage.  This is not an
        overall memory usage limit -- actual memory usage will surely be much
        higher than this.

Usage:
  bxh_event2table [opts] eventfiles...

This program takes XML event files as input, selects events (given
user-specified queries), and writes a table of these events and associated
metadata to standard output.  Each row is one event, and each column represents
a different metadata element (like onset, duration, and other values specified
in the events file).

  --version
        Print version string and exit.
  --optsfromfile <str>
  --optsfromfile=<str>
        Program options (i.e. those starting with '--') will come from this
        file.  If this option is specified, then the options in the file will
        be applied after all command-line options.  The options (and their
        arguments) should be specified one per line, with the leading '--'
        omitted.
  --querylanguage <str>
  --querylanguage=<str>
        The language used for all queries.  Valid values are 'XPath' and
        'event'.  Case is irrelevant.  Default is 'XPath'.
  --query <str>
  --query=<str>
        A query string to match events.  This option is required.
  --filterquery <str>
  --filterquery=<str>
        A query string to filter matched events.
  --colsep <str>
  --colsep=<str>
        String to separate columns (default is tab).

Usage:
  bxh_eventmerge [ --debug ] [ --eventpath XPATH ] [ --mergeeventpath XPATH ] [ --mergequery XPATH ] [ --grabincludeset XPATH ] [ --grabexcludeset XPATH ] INPUTQUERY GRABQUERY inputevents1.xml inputevents2.xml... mergeevents.xml

This program takes several input files (inputevents*.xml) and "merges"
the information from another event file (mergeevents.xml) into each input
file.  Here is the algorithm:

1. Create sets of event nodes in the input and merge event files using the
   XPaths specified by --eventpath and --mergeeventpath.  Default for
   --eventpath, if not specified, is //events/event (but namespace-agnostic),
   and default for --mergeeventpath is the specified or default value of the
   --eventpath option.
2. Each event node in the input event files will have a "match" value created
   by applying the XPath INPUTQUERY.
3. Each event node in the merge event file will have a "match" value created
   by applying the XPath specified by the --mergequery option (which is set to
   INPUTQUERY by default).
4. For each event node in the input event file whose "match" value is
   not an empty string, and which matches the "match" value of an event node
   in the merge event file:
   a. Apply GRABQUERY to the matching merge event, and recursively copy every
      node in the result set, *but*:
      i.  if --grabincludeset is specified, only include those nodes that are
          also in the set created by applying the XPath specified by
          --grabincludeset to the merge event.
      ii. if --grabexcludeset is specified, exclude those nodes that are
          also in the set created by applying the XPath specified by
          --grabexcludeset to the merge event.
5. All non-matching events in the input files will be output without
   change.

The output files will be named the same as the inputs, but starting
with the prefix "merged-".

Usage:
  bxh_eventresp [opts] eventfiles... outputfile

This program takes event files as input, and selects stimulus and response
events (given user-specified queries).  The responses are then merged into the
closest stimulus event within a given time interval from the response.

  --version
        Print version string and exit.
  --optsfromfile <str>
  --optsfromfile=<str>
        Program options (i.e. those starting with '--') will come from this
        file.  If this option is specified, then the options in the file will
        be applied after all command-line options.  The options (and their
        arguments) should be specified one per line, with the leading '--'
        omitted.
  --overwrite
        Overwrite existing output files (otherwise error and exit). 
  --querylanguage <str>
  --querylanguage=<str>
        The language used for all queries.  Valid values are 'XPath' and
        'event'.  Case is irrelevant.  Default is 'XPath'.
  --stimquery <str>
  --stimquery=<str>
        A query string to match stimulus events.  This option is required.
  --stimfilterquery <str>
  --stimfilterquery=<str>
        A query string to filter stimulus events.
  --respquery <str>
  --respquery=<str>
        A query string to match response events.  This option is required.
  --respfilterquery <str>
  --respfilterquery=<str>
        A query string to filter stimulus events.
  --maxresptime <double>
  --maxresptime=<double>
        Specifies the longest time interval (in the same units as the onsets in
        the input file) within which a response can be associated with a
        stimulus.  A negative value represents infinity (default).
  --respdelayname <str>
  --respdelayname=<str>
        The name to be used to label the value for response delay (time of
        response minus time of stimulus).  Default is not to add this value.
  --embeddedrespdelayvalues <str>
  --embeddedrespdelayvalues=<str>
        If the actual response delay is embedded within (and relative to) an
        event that is not strictly a response event, this option lists the
        names of the <value> elements (separated by commas) in the
        (pseudo-)response events that would store the response delay.  Only one
        value within each event may match this list.  This value will be added
        to the default response delay (response event time minus stimulus event
        time) to calculate the actual response time/delay.
  --movevalue <str>
  --movevalue=<str>
        By default, all values are moved from matched responses to matched
        stimuli.  If this option is specified one or more times, only the
        values specified by instances of this option will be moved.  Other
        values will be left alone.
  --reversemerge
        This option reverses the merging process -- instead of moving response
        event values into matching stimulus events, it will move the matching
        stimulus event's values into the response event.  The response delay
        value (if --respdelayname is specified) is also put into the response
        event.  Make sure this is what you really want to do!

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Usage:
  bxh_mean [opts] inputs.bxh... output.bxh

This program calculates per-voxel averages across a selected dimension, and
produces an output dataset 'collapsed' across that dimension.  If --dimension
'dataset' is specified, then corresponding voxels in each input dataset are
averaged to create an output dataset of the same dimensionality; in this case,
all of the dimensions in all input datasets must match.  If multiple input
datasets are provided and --dimension 'dataset' is not specified, then they are
concatenated along the last (slowest-moving) dimension; i.e. if one specifies
an XYZT 64x64x27x120 time series and an XYZT 64x64x27x130 time series as
inputs, they will be considered together as a single 64x64x27x250 time series.
In this case, all dimensions except the last dimension must match in all data
sets.

  --version
        Print version string and exit.
  --stddev <str>
  --stddev=<str>
        Calculate standard deviation too, and put the output in this file.
  --sumonly
        Calculate only the sum of the data, and don't divide by the number of
        inputs.  This option can not be used with --stddev.
  --dimension <str>
  --dimension=<str>
        Select the dimension over which to average.  The dimension must be one
        that exists in the input dataset, or must be 'dataset'.  Default is the
        last (slowest-moving) dimension.
  --outtype <str>
  --outtype=<str>
        The output will be of this type.  Valid types are: float64, float32,
        uint32, int32, uint16, int16, uint8, int8.  Note: using this option may
        result in overflow/underflow or precision errors if the output type can
        not represent the output appropriately.  Default is float64 if either
        of the inputs are float64, or float32 otherwise.

Usage:
  bxh_tfilter [opts] input.bxh output.bxh

This program runs, on a 4-D data set, a Chebyshev filter across each voxel's
fourth dimension (e.g. time course) and writes the results to output.bxh.

  --version
        Print version string and exit.
  --overwrite
        Overwrite existing output files (otherwise error and exit). 
  --filtertype <str>
  --filtertype=<str>
        This required option chooses the filter type.  Valid choices are
        'lowpass', 'highpass', 'bandpass, or 'bandstop'.  Each filter is
        parameterized by one or more instances of --period.  'lowpass' or
        'highpass' require one --period option, specifying the stop or start
        frequency respectively.  'bandpass' or 'bandstop' require two --period
        options, specifying the start and stop frequencies, in any order
        (larger period/smaller frequency is assumed to be start frequency for
        'bandpass' and stop frequency for 'bandstop').
  --period <double>
  --period=<double>
        This option specifies the frequency parameters for the filter in terms
        of the period (i.e. 1/frequency) in seconds per cycle.  May be
        specified once for 'lowpass' and 'highpass' filter types, twice for
        'bandpass' and 'bandstop' filter types, and must be greater than 0.
  --ripple <double>
  --ripple=<double>
        This option specifies the percent ripple for the Chebyshev filter.  If
        0 [zero], which is the default, then the filter is a Butterworth
        filter.
  --order <uint>
  --order=<uint>
        Order of the filter.  Default is 6.
  --forcetr <double>
  --forcetr=<double>
        If specified, this value (in seconds) will replace the TR specified in
        the input image file, if any.
  --keepdc
        Keep DC component (mean signal).  Has no effect for lowpass and
        bandpass filter types (which already keep the DC component).

Usage:
  bxh_ttest [opts] avg1.bxh std1.bxh n1.bxh avg2.bxh std2.bxh n2.bxh out_tfile

This program computes a per-voxel t-statistic between two datasets given their
3-D or 4-D mean, standard deviation, and n images.  Output (in out_tfile) is a
data set, with the same dimensions as the input, storing the t-statistic.

  --version
        Print version string and exit.
  --optsfromfile <str>
  --optsfromfile=<str>
        Program options (i.e. those starting with '--') will come from this
        file.  If this option is specified, then the options in the file will
        be applied after all command-line options.  The options (and their
        arguments) should be specified one per line, with the leading '--'
        omitted.
  --overwrite
        Overwrite existing output files (otherwise error and exit). 
  --timeselect <str>
  --timeselect=<str>
        Comma-separated list of timepoints to use (first timepoint is 0).  Any
        timepoint can be a contiguous range, specified as two numbers separated
        by a colon, i.e. 'START:END'.  An empty END implies the last timepoint.
        The default step of 1 (one) in ranges can be changed using
        'START:STEP:END', which is equivalent to
        'START,START+STEP,START+(2*STEP),...,END'.  Default is all timepoints
        (:).
  --xselect <str>
  --xselect=<str>
        Just like timeselect, but for the 'x' dimension.
  --yselect <str>
  --yselect=<str>
        Just like timeselect, but for the 'y' dimension.
  --zselect <str>
  --zselect=<str>
        Just like timeselect, but for the 'z' dimension.
  --maskfile <str>
  --maskfile=<str>
        Use this 3-D mask (should be an XML file) before doing calculations.

Usage:
  bxhabsorb [ --fromtype type ] [ type-specific-opts... ] inputfiles...
bxhoutputfile
  bxhabsorb [ --fromtype type ] [ --inputsfromfile inputlistfile ] [
type-specific-opts...] bxhoutputfile

This program creates a BXH or XCEDE wrapper for the specified input images.  If
the --fromtype option is not specified, it attempts to auto-detect the format
of the input image files.  If it cannot auto-detect the format, it will exit
with an error.
  --fromtype <str>
  --fromtype=<str>
        Type of the input data (pfile, signa5, signafive, iowa-signa5,
        iowa-signafive, ximg, analyze, afni, nrrd, dicom).  If this option is
        not specified, attempt to autodetect format of inputfiles.
  --inputsfromfile <str>
  --inputsfromfile=<str>
        Read list of input files from this file.
  --version
        Print version string and exit.
  --hintsizex <size_t>
  --hintsizex=<size_t>
  --hintsizey <size_t>
  --hintsizey=<size_t>
  --hintsizez <size_t>
  --hintsizez=<size_t>
  --hintsizet <size_t>
  --hintsizet=<size_t>
  --hintoriginx <double>
  --hintoriginx=<double>
  --hintoriginy <double>
  --hintoriginy=<double>
  --hintoriginz <double>
  --hintoriginz=<double>
  --hintorigint <double>
  --hintorigint=<double>
  --hintspacingx <double>
  --hintspacingx=<double>
  --hintspacingy <double>
  --hintspacingy=<double>
  --hintspacingz <double>
  --hintspacingz=<double>
  --hintspacingt <double>
  --hintspacingt=<double>
  --hintgapx <double>
  --hintgapx=<double>
  --hintgapy <double>
  --hintgapy=<double>
  --hintgapz <double>
  --hintgapz=<double>
  --hintgapt <double>
  --hintgapt=<double>
        These options will provide a hint to the program of the 'size',
        'origin', 'spacing', or 'gap' of the specified dimension.  Some image
        types will not use all these values.  In particular, sizex and sizey
        are assumed correct in most image headers, but they, as well as sizez
        and sizet options may be useful with image type 'pfile'.  Origin and
        spacing hints will be used by most image types.  
  --forceorientation <str>
  --forceorientation=<str>
        This option will force the labeled orientation of the image to match
        the given three letter orientation code.  Each letter must come from
        the following groups in any order: R(ight) or L(eft); A(nterior) or
        P(osterior); S(uperior) or I(nferior).  Only one letter from each group
        is allowed.
  --xcede
        Write XCEDE-style XML files.
  --xcede2
        Write XCEDE 2-style XML files.

PFILE USAGE 
  bxhabsorb --fromtype pfile [opts] [pfilehdr imagedata1...] output.bxh
PFILE OPTIONS 
  --forceversion <float>
  --forceversion=<float>
        Force version of P-file to be interpreted as this number.
  --msbfirst
        Indicates that data is big-endian (default: little-endian).
  --dimorder <str>
  --dimorder=<str>
        Comma-separated names of dimensions from fastest-moving to
        slowest-moving (default: x,y,z,t).
  --elemtype <str>
  --elemtype=<str>
        Provide element type of image data (one of int8, uint8, int16
        [default], uint16, int32, uint32, float32, or float64).
  --usemrorigin
        This option extracts the origin from the tlhc_[RAS] fields in the MR
        structure.  This is the default.
  --useslicetableorigin
        The origin coordinates are extracted from the slice table at the end of
        the P-file header.

SIGNA 5.X USAGE 
  bxhabsorb --fromtype signa5 [opts] [signa5files...] output.bxh
  bxhabsorb --fromtype signafive [opts] [signa5files...] output.bxh
SIGNA 5.X OPTIONS 
  --dimzsize <size_t>
  --dimzsize=<size_t>
        Specifies the size of the z dimension (i.e. number of slices per
        timepoint).  Default is to use the number of input files.  Equivalent
        to (and overrides) --hintsizez.
  --dimtsize <size_t>
  --dimtsize=<size_t>
        Specifies the size of the t dimension (i.e. number of timepoints).
        Default is number of input files divided by number of slices per
        timepoint (as specified by --dimzsize).  Equivalent to (and overrides)
        --hintsizet.

IOWA SIGNA 5.X USAGE 
  bxhabsorb --fromtype iowa-signa5 imagedir output.bxh
  bxhabsorb --fromtype iowa-signafive imagedir output.bxh
  NOTE: the bxhabsorb option --inputsfromfile is not available for the
  iowa-signa5 format
 imagedir is a directory containing I.* images

XIMG USAGE 
  bxhabsorb --fromtype ximg [opts] [ximgfiles...] output.bxh
XIMG OPTIONS 
  --dimzsize <size_t>
  --dimzsize=<size_t>
        Specifies the size of the z dimension (i.e. number of slices per
        timepoint).  Default is to use the number of input files.  Equivalent
        to (and overrides) --hintsizez.
  --dimtsize <size_t>
  --dimtsize=<size_t>
        Specifies the size of the t dimension (i.e. number of timepoints).
        Default is number of input files divided by number of slices per
        timepoint (as specified by --dimzsize).  Equivalent to (and overrides)
        --hintsizet.

ANALYZE/SPM USAGE 
  bxhabsorb --fromtype analyze [opts] [analyzefiles...] output.bxh
ANALYZE/SPM OPTIONS:
  --orientation <str>
  --orientation=<str>
        Orientation of image, letters indication which way theX, Y, and Z
        dimensions (in that order) are pointing (e.g. LPS, IRP).  Default is
        RAS (i.e. orientation used by SPM), or that specified in accompanying
        SPM .mat files.  This option overrides all info in SPM .mat files
        and/or the Analyze 'orient' field (if --strictanalyze is specified).
        Equivalent to (and overrides) --forceorientation.
  --strictanalyze
        Don't use SPM .mat files and use Analyze convention for orientation.
        The 'orient' field in the analyze header is parsed, and the default
        case (i.e. it is zero) means 'LAS'.
  --avwbyteorder <str>
  --avwbyteorder=<str>
        Specify byte order for AVW files (which don't store this info). This
        field should be 'l' for little-endian or 'b' for big-endian.

AFNI USAGE 
  bxhabsorb --fromtype afni [opts] afnifile.HEAD output.bxh

NRRD USAGE 
  bxhabsorb --fromtype nrrd [opts] file.nrrd output.bxh
    bxhabsorb --fromtype nrrd [opts] file.nhdr output.bxh


DICOM USAGE 
  bxhabsorb --fromtype dicom [opts] [dicomfiles...] output.bxh
general options:
  --debug
  -d
        debug mode, print debug information
input options:
  --force-concat
        If the input images have different orientation, Study UID, Series UID,
        ImageType, etc., then this option nevertheless forces them to be
        concatenated into the same volume.  (They would otherwise be
        encapsulated within separate XML files.)  This option may result in XML
        files that do not correctly describe the DICOM data -- use only if you
        know what you're doing!
  --filename-sort
        This program normally sorts input files by various fields in the DICOM
        headers.  This option forces a sort by filename only.  This can be
        useful in the case that the fields are unreliable.
  --no-sort
        This program normally sorts input files by various fields in the DICOM
        headers.  This option disables sorting and relies on the order in which
        files are provided on the command line.  This can be useful in the case
        that the fields are unreliable.
   input file format:
  --search-for-others
  -s
        search for matching files in the same directory
  --read-dataset
  -f
        read data set without file meta information
 input transfer syntax (only with --read-dataset):
  --read-xfer-auto
  -t
        use TS recognition (default)
  --read-xfer-little
  -te
        read with explicit VR little endian TS
  --read-xfer-big
  -tb
        read with explicit VR big endian TS
  --read-xfer-implicit
  -ti
        read with implicit VR little endian TS
output options:
 converting:
  --load-short
  -M
        do not load very long values (e.g. pixel data)
 error handling:
  --ignore-errors
  -E
        attempt to convert even if file is damaged

MGH/MGZ USAGE 
  bxhabsorb --fromtype mgh [opts] file.mgh output.bxh
  bxhabsorb --fromtype mgh [opts] file.mgz output.bxh

BXH/XCEDE (as input) USAGE 
  bxhabsorb --fromtype bxh [opts] bxhfile outputfile
    bxhabsorb --fromtype xcede [opts] xcedefile outputfile

Usage:
  bxhreorient [options] inputfile [ outputfile [datafileout] ]

This program reorients the image data given by the input BXH or XCEDE file to
an orientation specified by the user using the --orientation option.  It is
assumed that the orientation vectors in the BXH/XCEDE file are correct with
respect to the image data.  outputfile is required if not using --inplace
option.  Output is also a BXH or XCEDE file, pointing to an image data file
(named by datafileout if specified).

  --version
        Print version string and exit.
  --overwrite
        Overwrite output files if they exist.
  --orientation <str>
  --orientation=<str>
        This option specifies the new orientation by R/L A/P S/I letters,
        upper- or lower-case, in X,Y,Z order, where R means that dimension
        starts on the left and goes TO THE RIGHT, A means the dimension goes
        from posterior TO ANTERIOR, etc.  For example, IPR means X goes S->I, Y
        goes A->P, and Z goes L->R.  Default is RAS (neurological axial, as
        used by SPM).

Usage:
  bxhselect [options] inputfile outputfile

This program copies a subset of the input image data based on the various
selection options.  The selected subset is written to the output file.

  --version
        Print version string and exit.
  --timeselect <str>
  --timeselect=<str>
        Comma-separated list of timepoints to use (first timepoint is 0).  Any
        timepoint can be a contiguous range, specified as two numbers separated
        by a colon, i.e. 'START:END'.  An empty END implies the last timepoint.
        The default step of 1 (one) in ranges can be changed using
        'START:STEP:END', which is equivalent to
        'START,START+STEP,START+(2*STEP),...,END'.
  --xselect <str>
  --xselect=<str>
        Just like timeselect, but for the 'x' dimension.
  --yselect <str>
  --yselect=<str>
        Just like timeselect, but for the 'y' dimension.
  --zselect <str>
  --zselect=<str>
        Just like timeselect, but for the 'z' dimension.
  --overwrite
        Overwrite output files if they exist.

Usage:
  bxhsetorient [options] orient inputfile [outputfile]

This program sets the orientation vectors in the BXH or XCEDE file.  NOTE: this
program does not reorient or otherwise touch the image data itself.  This
program is useful to fix incorrect or missing orientation vectors in a
BXH/XCEDE file.  bxhfileout is required if not using --inplace option (and
vice-versa).  'orient' specifies the new orientation by R/L A/P S/I letters,
upper- or lower-case, in X,Y,Z order, where R means that dimension starts on
the left and goes TO THE RIGHT, A means the dimension goes from posterior TO
ANTERIOR, etc.  For example, IPR means X goes S->I, Y goes A->P, and Z goes
L->R.

  --version
        Print version string and exit.
  --inplace
        Do the reorientation in-place, overwriting the original BXH file.

Usage:
  dicom2bxh [opts] [dicomfiles...] output.bxh

This program creates an XML wrapper for DICOM images.

general options:
  --debug
  -d
        debug mode, print debug information
input options:
  --force-concat
        If the input images have different orientation, Study UID, Series UID,
        ImageType, etc., then this option nevertheless forces them to be
        concatenated into the same volume.  (They would otherwise be
        encapsulated within separate XML files.)  This option may result in XML
        files that do not correctly describe the DICOM data -- use only if you
        know what you're doing!
  --filename-sort
        This program normally sorts input files by various fields in the DICOM
        headers.  This option forces a sort by filename only.  This can be
        useful in the case that the fields are unreliable.
  --no-sort
        This program normally sorts input files by various fields in the DICOM
        headers.  This option disables sorting and relies on the order in which
        files are provided on the command line.  This can be useful in the case
        that the fields are unreliable.
   input file format:
  --search-for-others
  -s
        search for matching files in the same directory
  --read-dataset
  -f
        read data set without file meta information
 input transfer syntax (only with --read-dataset):
  --read-xfer-auto
  -t
        use TS recognition (default)
  --read-xfer-little
  -te
        read with explicit VR little endian TS
  --read-xfer-big
  -tb
        read with explicit VR big endian TS
  --read-xfer-implicit
  -ti
        read with implicit VR little endian TS
output options:
 converting:
  --load-short
  -M
        do not load very long values (e.g. pixel data)
 error handling:
  --ignore-errors
  -E
        attempt to convert even if file is damaged
additional options:
  --inputsfromfile <str>
  --inputsfromfile=<str>
        Read list of input files from this file.
  --version
        Print version string and exit.
  --hintsizex <size_t>
  --hintsizex=<size_t>
  --hintsizey <size_t>
  --hintsizey=<size_t>
  --hintsizez <size_t>
  --hintsizez=<size_t>
  --hintsizet <size_t>
  --hintsizet=<size_t>
  --hintoriginx <double>
  --hintoriginx=<double>
  --hintoriginy <double>
  --hintoriginy=<double>
  --hintoriginz <double>
  --hintoriginz=<double>
  --hintorigint <double>
  --hintorigint=<double>
  --hintspacingx <double>
  --hintspacingx=<double>
  --hintspacingy <double>
  --hintspacingy=<double>
  --hintspacingz <double>
  --hintspacingz=<double>
  --hintspacingt <double>
  --hintspacingt=<double>
  --hintgapx <double>
  --hintgapx=<double>
  --hintgapy <double>
  --hintgapy=<double>
  --hintgapz <double>
  --hintgapz=<double>
  --hintgapt <double>
  --hintgapt=<double>
        These options will provide a hint to the program of the 'size',
        'origin', 'spacing', or 'gap' of the specified dimension.  Some image
        types will not use all these values.  In particular, sizex and sizey
        are assumed correct in most image headers, but they, as well as sizez
        and sizet options may be useful with image type 'pfile'.  Origin and
        spacing hints will be used by most image types.  
  --forceorientation <str>
  --forceorientation=<str>
        This option will force the labeled orientation of the image to match
        the given three letter orientation code.  Each letter must come from
        the following groups in any order: R(ight) or L(eft); A(nterior) or
        P(osterior); S(uperior) or I(nferior).  Only one letter from each group
        is allowed.
  --xcede
        Write XCEDE-style XML files.
  --xcede2
        Write XCEDE 2-style XML files.

Usage:
  dumpheader inputfile

This program prints a simplistic summary of the BXH or XCEDE file given as input.

Usage:
  eprime2xml instructions.txt eprime.txt [outputevents.xml]

eprime2xml takes an E-Prime output file as exported as text from
the E-Prime software and an instruction file, and creates an
XML event file.  The instruction file indicates which columns
in the E-Prime file are of interest and what they should map
to in the output event file.  If the output file is not specified,
the event data is written to standard output.
Options:
  --xcede2
        Write in XCEDE2 format.
  --xcede2dataid=ID
        ID for the XCEDE 2 data element (default: auto-generated based
        on hostname, process ID, and current time)
  --extracttable
        Instead of creating XML as output, output as tabular text.
        This is a no-op for most formats, and is really only useful for
        converting E-Prime "recovery" logs into a tabular form.
  --columnnames
        If this options is specified, only the columns of the table are
        printed (one per line) and the program exits.
  --subtractonset SECS
        This option subtracts SECS from all onset times (default is 0).
        This is in addition to any other normalization that may occur
        (see use of 'firstmritime' below).
  --colsep SEPARATOR
        This option specifies the column separator (default is tab).

The instruction file language is defined as follows:

 COMMAND VALUESPEC [VALUESPEC...]

where COMMAND can be event, param, or block.  VALUESPEC has one
of the following formats:

 [OUTVALUENAME=]COLUMNNAME[:UNITS]
 OUTVALUENAME=@TEXT[:UNITS]

Each VALUESPEC defines values that should be passed through to
the corresponding event, param, or block.  In the first alternative
listed above, the value comes from a column in the input file
(optionally renamed to OUTVALUENAME) and in the second
alternatives, the value is directly specified preceded by a '@' character.
If OUTVALUENAME= is missing, then the VALUESPEC is equivalent to:

 COLUMNNAME=COLUMNNAME[:UNITS]

OUTVALUENAME may not contain the equals sign ('='), at sign ('@'), quotes,
or whitespace.

Either COLUMNNAME or TEXT may contain quoted substrings to protect special
characters like colon (':'), equals sign ('='), at sign ('@'), or whitespace;
otherwise these special characters are prohibited.  A single quote will
protect all characters until the next single quote, and likewise for double
quote.  The following examples show equivalent VALUESPECs:

 description=DESC
 description=D'E'"SC"

 onset="Onset Time":secs
 onset=Onset' 'Time:secs
 onset=Onse't T'ime:secs

Unquoted spaces separate VALUESPECs.

----------------
'event' command:
----------------
Each 'event' command creates a class of events in the output
event file, where the contents of the event are specified by
the VALUESPECs.  In general, for each matching row (more later),
it creates an event with the following contents:

  <event type="$type" units="$units">
    <onset>$onset</onset>
    <duration>$duration</duration>
    <name>$name</name>
    <description>$description</description>
    <value name="OUTVALUENAME1" units="UNITS1">VALUE1</value>
    <value name="OUTVALUENAME2" units="UNITS2">VALUE2</value>
    ...
  </event>

VALUESPECs whose OUTVALUENAMEs start with a dollar sign ( $ ) are
"magic", and are interpreted in a value-specific way.  VALUESPECs
whose OUTVALUENAMEs start with a percent sign ( % ) are explicitly
non-magic.  Any OUTVALUENAME not starting with a % or $ is
is assumed to have an implicit % unless it matches a list of
pre-defined magic values (below), in which case an implicit $
is assumed.

Pre-defined magic values '$type', '$units', '$onset', '$duration',
'$name', and '$description' are put in the appropriate child element
or attribute of <event> (shown above).  Only the '$onset' VALUESPEC
is required.  Default value for '$duration' is zero.  All non-magic
values are placed in <value> elements.

The pre-defined magic value '$DURUNTIL' indicates that any row in the
input used to create an event will have an ending time specified by
the value of column COLUMNNAME in the current row.  Likewise, the
value '$DURUNTILNEXTROW' does the same thing, but grabs the value from
the next row.  These are used to calculate the duration of this event.
This may be specified more than once, and the first non-NULL column
will be used.  This option is used when a row does not have a duration
column, and it must be calculated based on times in this or the
subsequent row.

By default, only those rows whose '$onset' column is non-empty and
non-NULL will be processed as events.  Certain magic OUTVALUENAMEs
further restrict the rows that are used for this event command.
'$MATCH' and '$MATCHNONZERO' specify a column whose values indicate
whether that row should be selected -- for '$MATCH', the values must
be non-empty and non-'NULL'; for '$MATCHNONZERO', the values must also
be non-zero.  With '$MATCHEQUAL', one specifies both a column and an
actual value to match -- for the '$MATCHEQUAL' value name (and only
the '$MATCHEQUAL' value name) the VALUESPEC syntax is extended in the
following way:

 $MATCHEQUAL=COLUMNNAME@MATCHVALUE

where COLUMNNAME and MATCHVALUE are the two relevant parameters.

----------------
'block' command:
----------------
The block command has the same usage as the event command.
The same magic values apply to block commands as event commands.
An '$onset' value is again required, and '$duration' is
optional (assumed to be zero [0] if missing).

----------------
'param' command:
----------------
Each param command specifies a list of columns that should be
put in the <params> section of the event file.  These represent
parameters that are constant (or default) throughout the events
file.  Each VALUESPEC represents one item to put in the <params>
element as such:

  <params>
    ...
    <value name="OUTVALUENAME1" units="UNITS1">VALUE1</value>
    <value name="OUTVALUENAME2" units="UNITS2">VALUE2</value>
    ...
  </params>

Only the first non-empty, non-NULL field in the column specified by a
'param' will be used.  Be aware of this if this column does not have
the same value in every row.

There is one magic OUTVALUENAME (maybe more later) '$firstmritime',
which will generate the following element:

  <params>
    <firstmritime>0</firstmritime>
  </params>

If '$firstmritime' is specified, it (and all '$onset' VALUESPECs)
must have UNITS specified.  All '$onset' columns are normalized
by this value, so their units and '$firstmritime' units must match.

Usage:
  eventstable2xml instructions.txt inputevents.txt [outputevents.xml]

eventstable2xml takes a text tabular events file and an instruction
file, and creates an XML events file.  The instruction file indicates
which columns in the original events file are of interest and what
they should map to in the output event file.  If the output file is
not specified, the event data is written to standard output.
Options:
  --xcede2
        Write in XCEDE2 format.
  --xcede2dataid=ID
        ID for the XCEDE 2 data element (default: auto-generated based
        on hostname, process ID, and current time)
  --extracttable
        Instead of creating XML as output, output as tabular text.
        This is a no-op for most formats, and is really only useful for
        converting E-Prime "recovery" logs into a tabular form.
  --columnnames
        If this options is specified, only the columns of the table are
        printed (one per line) and the program exits.
  --subtractonset SECS
        This option subtracts SECS from all onset times (default is 0).
        This is in addition to any other normalization that may occur
        (see use of 'firstmritime' below).
  --colsep SEPARATOR
        This option specifies the column separator (default is tab).

The instruction file language is defined as follows:

 COMMAND VALUESPEC [VALUESPEC...]

where COMMAND can be event, param, or block.  VALUESPEC has one
of the following formats:

 [OUTVALUENAME=]COLUMNNAME[:UNITS]
 OUTVALUENAME=@TEXT[:UNITS]

Each VALUESPEC defines values that should be passed through to
the corresponding event, param, or block.  In the first alternative
listed above, the value comes from a column in the input file
(optionally renamed to OUTVALUENAME) and in the second
alternatives, the value is directly specified preceded by a '@' character.
If OUTVALUENAME= is missing, then the VALUESPEC is equivalent to:

 COLUMNNAME=COLUMNNAME[:UNITS]

OUTVALUENAME may not contain the equals sign ('='), at sign ('@'), quotes,
or whitespace.

Either COLUMNNAME or TEXT may contain quoted substrings to protect special
characters like colon (':'), equals sign ('='), at sign ('@'), or whitespace;
otherwise these special characters are prohibited.  A single quote will
protect all characters until the next single quote, and likewise for double
quote.  The following examples show equivalent VALUESPECs:

 description=DESC
 description=D'E'"SC"

 onset="Onset Time":secs
 onset=Onset' 'Time:secs
 onset=Onse't T'ime:secs

Unquoted spaces separate VALUESPECs.

----------------
'event' command:
----------------
Each 'event' command creates a class of events in the output
event file, where the contents of the event are specified by
the VALUESPECs.  In general, for each matching row (more later),
it creates an event with the following contents:

  <event type="$type" units="$units">
    <onset>$onset</onset>
    <duration>$duration</duration>
    <name>$name</name>
    <description>$description</description>
    <value name="OUTVALUENAME1" units="UNITS1">VALUE1</value>
    <value name="OUTVALUENAME2" units="UNITS2">VALUE2</value>
    ...
  </event>

VALUESPECs whose OUTVALUENAMEs start with a dollar sign ( $ ) are
"magic", and are interpreted in a value-specific way.  VALUESPECs
whose OUTVALUENAMEs start with a percent sign ( % ) are explicitly
non-magic.  Any OUTVALUENAME not starting with a % or $ is
is assumed to have an implicit % unless it matches a list of
pre-defined magic values (below), in which case an implicit $
is assumed.

Pre-defined magic values '$type', '$units', '$onset', '$duration',
'$name', and '$description' are put in the appropriate child element
or attribute of <event> (shown above).  Only the '$onset' VALUESPEC
is required.  Default value for '$duration' is zero.  All non-magic
values are placed in <value> elements.

The pre-defined magic value '$DURUNTIL' indicates that any row in the
input used to create an event will have an ending time specified by
the value of column COLUMNNAME in the current row.  Likewise, the
value '$DURUNTILNEXTROW' does the same thing, but grabs the value from
the next row.  These are used to calculate the duration of this event.
This may be specified more than once, and the first non-NULL column
will be used.  This option is used when a row does not have a duration
column, and it must be calculated based on times in this or the
subsequent row.

By default, only those rows whose '$onset' column is non-empty and
non-NULL will be processed as events.  Certain magic OUTVALUENAMEs
further restrict the rows that are used for this event command.
'$MATCH' and '$MATCHNONZERO' specify a column whose values indicate
whether that row should be selected -- for '$MATCH', the values must
be non-empty and non-'NULL'; for '$MATCHNONZERO', the values must also
be non-zero.  With '$MATCHEQUAL', one specifies both a column and an
actual value to match -- for the '$MATCHEQUAL' value name (and only
the '$MATCHEQUAL' value name) the VALUESPEC syntax is extended in the
following way:

 $MATCHEQUAL=COLUMNNAME@MATCHVALUE

where COLUMNNAME and MATCHVALUE are the two relevant parameters.

----------------
'block' command:
----------------
The block command has the same usage as the event command.
The same magic values apply to block commands as event commands.
An '$onset' value is again required, and '$duration' is
optional (assumed to be zero [0] if missing).

----------------
'param' command:
----------------
Each param command specifies a list of columns that should be
put in the <params> section of the event file.  These represent
parameters that are constant (or default) throughout the events
file.  Each VALUESPEC represents one item to put in the <params>
element as such:

  <params>
    ...
    <value name="OUTVALUENAME1" units="UNITS1">VALUE1</value>
    <value name="OUTVALUENAME2" units="UNITS2">VALUE2</value>
    ...
  </params>

Only the first non-empty, non-NULL field in the column specified by a
'param' will be used.  Be aware of this if this column does not have
the same value in every row.

There is one magic OUTVALUENAME (maybe more later) '$firstmritime',
which will generate the following element:

  <params>
    <firstmritime>0</firstmritime>
  </params>

If '$firstmritime' is specified, it (and all '$onset' VALUESPECs)
must have UNITS specified.  All '$onset' columns are normalized
by this value, so their units and '$firstmritime' units must match.

Usage:
  extractimagedata [opts] xmlfile outputfile

This program extracts the image data pointed to by the input BXH or XCEDE file
and writes it to outputfile.

  --version
        Print version string and exit.
  --msbfirst
        Extract data as big-endian (default: little-endian).

Usage:
  extractxyztdata [opts] xmlfile outputfile

This program extracts the image data pointed to by the input BXH or XCEDE file
and writes it to outputfile.  The data is reordered so that the dimensions
labeled 'x', 'y', 'z', and 't' are in that order.

  --version
        Print version string and exit.
  --msbfirst
        Extract data as big-endian (default: little-endian).

Usage:
  ffile2bxh [ --dimorder "x,y,z,t" ] ffile [datafile1...] outputfile

This program takes a Stanford F-file and creates a BXH or XCEDE header using
the metadata in the F-file, and points to the image data in the given
datafiles.
  --dimorder specifies the comma-separated names of the dimensions in the
             datafiles(s) in order from fastest-moving to slowest-moving
             Default is "x,y,z,t".

  --xcede produces an XCEDE file as output.

Usage:
  fmriqa_count inputfile

This program outputs histograms or counts of voxels in a BXH- or XCEDE-wrapped
dataset that match the given conditions.  Output can be per-slice, per-volume,
or for entire dataset (see --granularity).  Histogram output requires the
--histogram option.  If histogram output is not chosen, output is as if there
were one histogram 'bucket'.  Conditions are specified as command-line options,
described below.  Default is to 'and' all conditions (but see --aggregate).
Default condition for 'and' aggregate is to match all voxels.Default condition
for 'or' aggregate is to match no voxels.  Thus, with no options, this program
prints out the number of voxels in the data.

  --version
        Print version string and exit.
  --granularity <str>
  --granularity=<str>
        Print counts at this granularity.  Acceptable values are 'timeseries'
        (default), 'volume', 'slice', and 'voxel'.
  --aggregate <str>
  --aggregate=<str>
        Conditions are aggregated by this operator, either 'and' (default) or
        'or'.
  --gt <double>
  --gt=<double>
        Match those voxels greater than this value.
  --ge <double>
  --ge=<double>
        Match those voxels greater than or equal to this value.
  --lt <double>
  --lt=<double>
        Match those voxels less than this value.
  --le <double>
  --le=<double>
        Match those voxels less than or equal to this value.
  --timeselect <str>
  --timeselect=<str>
        Match only those timepoints in this comma-separated list of timepoints
        (first timepoint is 0).  Any timepoint can be a contiguous range,
        specified as two numbers separated by a colon, i.e. 'START:END'.  An
        empty END implies the last timepoint.  The default step of 1 (one) in
        ranges can be changed using 'START:STEP:END', which is equivalent to
        'START,START+STEP,START+(2*STEP),...,END'.
  --xselect <str>
  --xselect=<str>
        Just like timeselect, but for the 'x' coordinate.
  --yselect <str>
  --yselect=<str>
        Just like timeselect, but for the 'y' coordinate.
  --zselect <str>
  --zselect=<str>
        Just like timeselect, but for the 'z' coordinate.
  --histogram
        Specifies that output should be histogram.  See --histobuckets to
        specify number of buckets, --histobucketwidth to specify width of
        buckets, or --histobounds to specify bucket boundaries.
  --histobuckets <int>
  --histobuckets=<int>
        Valid only with --histogram option.  Constructs this many evenly-spaced
        histogram buckets.  This option is incompatible with --histobounds or
        --histobucketwidth.
  --histobounds <str>
  --histobounds=<str>
        Valid only with --histogram option.  By default, histogram bucket
        boundaries are in multiples of standard deviations.  This option
        specifies alternate boundaries for (N + 1) buckets as a space-separated
        list of N floating point numbers.  For example, --histobounds "0.0 5.0
        10.0" will separate voxels with values -infinity < x < 0.0, 0.0 <= x <
        5.0, 5.0 <= x < 10.0, and 10.0 <= x < infinity.  This option is
        incompatible with --histobucketwidth or --histobucketsize.
  --histobucketwidth <double>
  --histobucketwidth=<double>
        Valid only with --histogram option.  Constructs evenly-spaced histogram
        buckets with this width.  This option is incompatible with
        --histobounds or --histobuckets.

Can't locate BXHPerlUtils.pm in @INC (@INC contains: /builddir/build/BUILD/RELEASE_1_10_7/bxh_xcede_tools/fmriqa /usr/local/lib/perl5 /usr/local/share/perl5 /usr/lib/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib/perl5 /usr/share/perl5 .) at ../../fmriqa/fmriqa_generate.pl line 39.
BEGIN failed--compilation aborted at ../../fmriqa/fmriqa_generate.pl line 39.

Usage:
  fmriqa_minmax xmlfile(s)...

This program merely computes the minimum and maximum values in the input
BXH- or XCEDE-wrapped dataset and writes them to standard output.

Usage:
  fmriqa_oediff [opts] xmlfile outputfile

Given a 4-D BXH- or XCEDE-wrapped time series, this program calculates the
cumulative difference between the even images (where the first selected image
is 0) and the odd images.  The input file must be BXH or XCEDE file, and the
output is a 3-D image in the same format, written to outputfile.

  --version
        Print version string and exit.
  --timeselect <str>
  --timeselect=<str>
        Comma-separated list of timepoints to use (first timepoint is 0).  Any
        timepoint can be a contiguous range, specified as two numbers separated
        by a colon, i.e. 'START:END'.  An empty END implies the last timepoint.
        The default step of 1 (one) in ranges can be changed using
        'START:STEP:END', which is equivalent to
        'START,START+STEP,START+(2*STEP),...,END'.
  --xselect <str>
  --xselect=<str>
        Just like timeselect, but for the 'x' dimension.
  --yselect <str>
  --yselect=<str>
        Just like timeselect, but for the 'y' dimension.
  --zselect <str>
  --zselect=<str>
        Just like timeselect, but for the 'z' dimension.

Can't locate BXHPerlUtils.pm in @INC (@INC contains: /builddir/build/BUILD/RELEASE_1_10_7/bxh_xcede_tools/fmriqa /usr/local/lib/perl5 /usr/local/share/perl5 /usr/lib/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib/perl5 /usr/share/perl5 .) at ../../fmriqa/fmriqa_phantomqa.pl line 32.
BEGIN failed--compilation aborted at ../../fmriqa/fmriqa_phantomqa.pl line 32.

Usage:
  fmriqa_phantomqa [opts] xmlfile [outputbase]

This program is usually called by fmriqa_phantomqa.pl, and is not likely to be
useful to users on its own.  This program takes a 4-D BXH- or XCEDE- wrapped
dataset and calculates and writes various QA measures, designed for fMRI images
of the BIRN calibration phantom.

  --version
        Print version string and exit.
  --timeselect <str>
  --timeselect=<str>
        Comma-separated list of timepoints to use (first timepoint is 0).  Any
        timepoint can be a contiguous range, specified as two numbers separated
        by a colon, i.e. 'START:END'.  An empty END implies the last timepoint.
        The default step of 1 (one) in ranges can be changed using
        'START:STEP:END', which is equivalent to
        'START,START+STEP,START+(2*STEP),...,END'.  Default is to ignore first
        2 timepoints (2:), or 3 if the total number of timepoints is odd.
  --zselect <str>
  --zselect=<str>
        Chooses the slice number on which to compute the statistics.  Must be a
        single unsigned integer within the range 0 <= x <= (numslices-1).
        Default is middle slice.
  --summaryonly
        Don't generate ave, nave, std images.
  --nofluct
        Don't run fluctuation analysis.
  --noroi
        Don't run ROI-based analysis.
  --roisize <uint>
  --roisize=<uint>
        Override the default ROI size of 30x30 (for 128x128 slices) or 15x15
        (for everything else).  Specify the length of the edge of the ROI box
        in voxels.
  --maskfile <str>
  --maskfile=<str>
        Use this mask (should be an XML file) instead of 30x30 (for 128x128
        slices) or 15x15 (or whatever is specified by --roisize).  If 2-D, must
        match slice dimensions of input data.  If 3-D, all three spatial
        dimensions must match (but only slice specified in zselect will be
        used).
  --forcetr <double>
  --forcetr=<double>
        If specified, this value (in seconds) will replace the TR specified in
        the input image file, if any.

Usage:
  fmriqa_spikiness [opts] xmlfile [outputbase]

This program is usually called by wrapper scripts, and may not be useful to
users on its own.  This program takes a 4-D BXH- or XCEDE- wrapped dataset and
calculates a 'spikiness' metric.  Various 'spikiness' metrics are available and
are selected using options.  The size and meaning of the output data is
dependent on the metric being calculated.

  --overwrite
        Overwrite output files if they exist.
  --version
        Print version string and exit.
  --verbose
        More diagnostic output.
  --metric <str>
  --metric=<str>
        Which metric to return after fitting/detrending data.
        'diff' returns (value-fit) per voxel.
        'zscore' returns (value-fit)/stddev per voxel.
        'abszscore' returns (value-fit)/stddev per voxel.
        'afni' returns abs(value-fit)/mstddev per voxel (i.e. same as returned
        by Robert Cox's AFNI 3dDespike) where mstddev is a modified standard
        deviation that is less influenced by outlier points.
        'abszscoreslice' returns average abs(value-fit)/stddev per slice.
        'jackknife' (default) takes the output of 'abszscoreslice' and finds
        the "jackknife" z-score of each slice (over the volume) where the
        current slice is ignored in calculating mean/stddev.
        'jackknife' and 'abszscoreslice' produce a 2-D result set, whereas
        every other metric produces a 4-D result set.
  --brainthresh <double>
  --brainthresh=<double>
        Only voxels with a value greater than its_brainthresh are used in the
        calculation.  Other voxels will return a metric of 0.  Default is minus
        infinity or thereabouts.
  --fit_method <str>
  --fit_method=<str>
        Which fitting/detrending method to use.
        'mean' (default) simply uses the mean of each voxel's time-course.
        'linear' does a linear L1 fit of each voxel time-course.
        'afni' L1-fits the function used in Robert Cox's AFNI 3dDespike program
        to each voxel's time-course.
  --timeselect <str>
  --timeselect=<str>
        Comma-separated list of timepoints to use (first timepoint is 0).  Any
        timepoint can be a contiguous range, specified as two numbers separated
        by a colon, i.e. 'START:END'.  An empty END implies the last timepoint.
        The default step of 1 (one) in ranges can be changed using
        'START:STEP:END', which is equivalent to
        'START,START+STEP,START+(2*STEP),...,END'.
  --xselect <str>
  --xselect=<str>
        Just like timeselect, but for the 'x' dimension.
  --yselect <str>
  --yselect=<str>
        Just like timeselect, but for the 'y' dimension.
  --zselect <str>
  --zselect=<str>
        Just like timeselect, but for the 'z' dimension.

Usage:
  iowa-signafive2bxh imagedir output.bxh

This program creates an XML wrapper for Univ. of Iowa-style GE Signa5 images.

 imagedir is a directory containing I.* images
  --xcede
        Write XCEDE-style XML files.
  --xcede2
        Write XCEDE 2-style XML files.

Usage:
  pfile2bxh [opts] [pfilehdr imagedata1...] output.bxh

This program creates an XML wrapper for GE P-files (and associated
reconstructed image data).

  --forceversion <float>
  --forceversion=<float>
        Force version of P-file to be interpreted as this number.
  --msbfirst
        Indicates that data is big-endian (default: little-endian).
  --dimorder <str>
  --dimorder=<str>
        Comma-separated names of dimensions from fastest-moving to
        slowest-moving (default: x,y,z,t).
  --elemtype <str>
  --elemtype=<str>
        Provide element type of image data (one of int8, uint8, int16
        [default], uint16, int32, uint32, float32, or float64).
  --usemrorigin
        This option extracts the origin from the tlhc_[RAS] fields in the MR
        structure.  This is the default.
  --useslicetableorigin
        The origin coordinates are extracted from the slice table at the end of
        the P-file header.
  --inputsfromfile <str>
  --inputsfromfile=<str>
        Read list of input files from this file.
  --version
        Print version string and exit.
  --hintsizex <size_t>
  --hintsizex=<size_t>
  --hintsizey <size_t>
  --hintsizey=<size_t>
  --hintsizez <size_t>
  --hintsizez=<size_t>
  --hintsizet <size_t>
  --hintsizet=<size_t>
  --hintoriginx <double>
  --hintoriginx=<double>
  --hintoriginy <double>
  --hintoriginy=<double>
  --hintoriginz <double>
  --hintoriginz=<double>
  --hintorigint <double>
  --hintorigint=<double>
  --hintspacingx <double>
  --hintspacingx=<double>
  --hintspacingy <double>
  --hintspacingy=<double>
  --hintspacingz <double>
  --hintspacingz=<double>
  --hintspacingt <double>
  --hintspacingt=<double>
  --hintgapx <double>
  --hintgapx=<double>
  --hintgapy <double>
  --hintgapy=<double>
  --hintgapz <double>
  --hintgapz=<double>
  --hintgapt <double>
  --hintgapt=<double>
        These options will provide a hint to the program of the 'size',
        'origin', 'spacing', or 'gap' of the specified dimension.  Some image
        types will not use all these values.  In particular, sizex and sizey
        are assumed correct in most image headers, but they, as well as sizez
        and sizet options may be useful with image type 'pfile'.  Origin and
        spacing hints will be used by most image types.  
  --forceorientation <str>
  --forceorientation=<str>
        This option will force the labeled orientation of the image to match
        the given three letter orientation code.  Each letter must come from
        the following groups in any order: R(ight) or L(eft); A(nterior) or
        P(osterior); S(uperior) or I(nferior).  Only one letter from each group
        is allowed.
  --xcede
        Write XCEDE-style XML files.
  --xcede2
        Write XCEDE 2-style XML files.

Usage:
  presentation2xml instructions.txt inputevents.txt [outputevents.xml]

presentation2xml takes a Presentation output file and an instruction
file, and creates an XML events file.  The instruction file indicates
which columns in the Presentation file are of interest and what
they should map to in the output event file.  If the output file is
not specified, the event data is written to standard output.
Options:
  --xcede2
        Write in XCEDE2 format.
  --xcede2dataid=ID
        ID for the XCEDE 2 data element (default: auto-generated based
        on hostname, process ID, and current time)
  --extracttable
        Instead of creating XML as output, output as tabular text.
        This is a no-op for most formats, and is really only useful for
        converting E-Prime "recovery" logs into a tabular form.
  --columnnames
        If this options is specified, only the columns of the table are
        printed (one per line) and the program exits.
  --subtractonset SECS
        This option subtracts SECS from all onset times (default is 0).
        This is in addition to any other normalization that may occur
        (see use of 'firstmritime' below).
  --colsep SEPARATOR
        This option specifies the column separator (default is tab).

The instruction file language is defined as follows:

 COMMAND VALUESPEC [VALUESPEC...]

where COMMAND can be event, param, or block.  VALUESPEC has one
of the following formats:

 [OUTVALUENAME=]COLUMNNAME[:UNITS]
 OUTVALUENAME=@TEXT[:UNITS]

Each VALUESPEC defines values that should be passed through to
the corresponding event, param, or block.  In the first alternative
listed above, the value comes from a column in the input file
(optionally renamed to OUTVALUENAME) and in the second
alternatives, the value is directly specified preceded by a '@' character.
If OUTVALUENAME= is missing, then the VALUESPEC is equivalent to:

 COLUMNNAME=COLUMNNAME[:UNITS]

OUTVALUENAME may not contain the equals sign ('='), at sign ('@'), quotes,
or whitespace.

Either COLUMNNAME or TEXT may contain quoted substrings to protect special
characters like colon (':'), equals sign ('='), at sign ('@'), or whitespace;
otherwise these special characters are prohibited.  A single quote will
protect all characters until the next single quote, and likewise for double
quote.  The following examples show equivalent VALUESPECs:

 description=DESC
 description=D'E'"SC"

 onset="Onset Time":secs
 onset=Onset' 'Time:secs
 onset=Onse't T'ime:secs

Unquoted spaces separate VALUESPECs.

----------------
'event' command:
----------------
Each 'event' command creates a class of events in the output
event file, where the contents of the event are specified by
the VALUESPECs.  In general, for each matching row (more later),
it creates an event with the following contents:

  <event type="$type" units="$units">
    <onset>$onset</onset>
    <duration>$duration</duration>
    <name>$name</name>
    <description>$description</description>
    <value name="OUTVALUENAME1" units="UNITS1">VALUE1</value>
    <value name="OUTVALUENAME2" units="UNITS2">VALUE2</value>
    ...
  </event>

VALUESPECs whose OUTVALUENAMEs start with a dollar sign ( $ ) are
"magic", and are interpreted in a value-specific way.  VALUESPECs
whose OUTVALUENAMEs start with a percent sign ( % ) are explicitly
non-magic.  Any OUTVALUENAME not starting with a % or $ is
is assumed to have an implicit % unless it matches a list of
pre-defined magic values (below), in which case an implicit $
is assumed.

Pre-defined magic values '$type', '$units', '$onset', '$duration',
'$name', and '$description' are put in the appropriate child element
or attribute of <event> (shown above).  Only the '$onset' VALUESPEC
is required.  Default value for '$duration' is zero.  All non-magic
values are placed in <value> elements.

The pre-defined magic value '$DURUNTIL' indicates that any row in the
input used to create an event will have an ending time specified by
the value of column COLUMNNAME in the current row.  Likewise, the
value '$DURUNTILNEXTROW' does the same thing, but grabs the value from
the next row.  These are used to calculate the duration of this event.
This may be specified more than once, and the first non-NULL column
will be used.  This option is used when a row does not have a duration
column, and it must be calculated based on times in this or the
subsequent row.

By default, only those rows whose '$onset' column is non-empty and
non-NULL will be processed as events.  Certain magic OUTVALUENAMEs
further restrict the rows that are used for this event command.
'$MATCH' and '$MATCHNONZERO' specify a column whose values indicate
whether that row should be selected -- for '$MATCH', the values must
be non-empty and non-'NULL'; for '$MATCHNONZERO', the values must also
be non-zero.  With '$MATCHEQUAL', one specifies both a column and an
actual value to match -- for the '$MATCHEQUAL' value name (and only
the '$MATCHEQUAL' value name) the VALUESPEC syntax is extended in the
following way:

 $MATCHEQUAL=COLUMNNAME@MATCHVALUE

where COLUMNNAME and MATCHVALUE are the two relevant parameters.

----------------
'block' command:
----------------
The block command has the same usage as the event command.
The same magic values apply to block commands as event commands.
An '$onset' value is again required, and '$duration' is
optional (assumed to be zero [0] if missing).

----------------
'param' command:
----------------
Each param command specifies a list of columns that should be
put in the <params> section of the event file.  These represent
parameters that are constant (or default) throughout the events
file.  Each VALUESPEC represents one item to put in the <params>
element as such:

  <params>
    ...
    <value name="OUTVALUENAME1" units="UNITS1">VALUE1</value>
    <value name="OUTVALUENAME2" units="UNITS2">VALUE2</value>
    ...
  </params>

Only the first non-empty, non-NULL field in the column specified by a
'param' will be used.  Be aware of this if this column does not have
the same value in every row.

There is one magic OUTVALUENAME (maybe more later) '$firstmritime',
which will generate the following element:

  <params>
    <firstmritime>0</firstmritime>
  </params>

If '$firstmritime' is specified, it (and all '$onset' VALUESPECs)
must have UNITS specified.  All '$onset' columns are normalized
by this value, so their units and '$firstmritime' units must match.

Usage:
  printfrags xmlfile

This program prints out the 'frags' in a BXH/XCEDE file.

Can't locate XML/Parser.pm in @INC (@INC contains: /builddir/build/BUILD/RELEASE_1_10_7/bxh_xcede_tools/utils /usr/local/lib/perl5 /usr/local/share/perl5 /usr/lib/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib/perl5 /usr/share/perl5 .) at /builddir/build/BUILD/RELEASE_1_10_7/bxh_xcede_tools/utils/XML/XPath/XMLParser.pm line 7.
BEGIN failed--compilation aborted at /builddir/build/BUILD/RELEASE_1_10_7/bxh_xcede_tools/utils/XML/XPath/XMLParser.pm line 7.
Compilation failed in require at /builddir/build/BUILD/RELEASE_1_10_7/bxh_xcede_tools/utils/XML/XPath.pm line 13.
BEGIN failed--compilation aborted at /builddir/build/BUILD/RELEASE_1_10_7/bxh_xcede_tools/utils/XML/XPath.pm line 13.
Compilation failed in require at ../../utils/showplay2xml line 13.
BEGIN failed--compilation aborted at ../../utils/showplay2xml line 13.

Usage:
  signafive2bxh [opts] [signa5files...] output.bxh

This program creates an XML wrapper for GE Signa5 image files.

  --dimzsize <size_t>
  --dimzsize=<size_t>
        Specifies the size of the z dimension (i.e. number of slices per
        timepoint).  Default is to use the number of input files.  Equivalent
        to (and overrides) --hintsizez.
  --dimtsize <size_t>
  --dimtsize=<size_t>
        Specifies the size of the t dimension (i.e. number of timepoints).
        Default is number of input files divided by number of slices per
        timepoint (as specified by --dimzsize).  Equivalent to (and overrides)
        --hintsizet.
  --inputsfromfile <str>
  --inputsfromfile=<str>
        Read list of input files from this file.
  --version
        Print version string and exit.
  --hintsizex <size_t>
  --hintsizex=<size_t>
  --hintsizey <size_t>
  --hintsizey=<size_t>
  --hintsizez <size_t>
  --hintsizez=<size_t>
  --hintsizet <size_t>
  --hintsizet=<size_t>
  --hintoriginx <double>
  --hintoriginx=<double>
  --hintoriginy <double>
  --hintoriginy=<double>
  --hintoriginz <double>
  --hintoriginz=<double>
  --hintorigint <double>
  --hintorigint=<double>
  --hintspacingx <double>
  --hintspacingx=<double>
  --hintspacingy <double>
  --hintspacingy=<double>
  --hintspacingz <double>
  --hintspacingz=<double>
  --hintspacingt <double>
  --hintspacingt=<double>
  --hintgapx <double>
  --hintgapx=<double>
  --hintgapy <double>
  --hintgapy=<double>
  --hintgapz <double>
  --hintgapz=<double>
  --hintgapt <double>
  --hintgapt=<double>
        These options will provide a hint to the program of the 'size',
        'origin', 'spacing', or 'gap' of the specified dimension.  Some image
        types will not use all these values.  In particular, sizex and sizey
        are assumed correct in most image headers, but they, as well as sizez
        and sizet options may be useful with image type 'pfile'.  Origin and
        spacing hints will be used by most image types.  
  --forceorientation <str>
  --forceorientation=<str>
        This option will force the labeled orientation of the image to match
        the given three letter orientation code.  Each letter must come from
        the following groups in any order: R(ight) or L(eft); A(nterior) or
        P(osterior); S(uperior) or I(nferior).  Only one letter from each group
        is allowed.
  --xcede
        Write XCEDE-style XML files.
  --xcede2
        Write XCEDE 2-style XML files.

Usage:
  xcede_extract_schedules.pl [OPTIONS] outputformat xmldir outputlocation queryfiles...
  xcede_extract_schedules.pl [OPTIONS] outputformat xmlfile outputlocation queryfiles...
  xcede_extract_schedules.pl [OPTIONS] outputformat xmlfile1,xmlfile2,... outputlocation queryfiles...
Values for 'outputformat':
  fsl -
    outputlocation should be a directory.  Output is one or more .stf files
    with base name derived from the conditions specified in the queryfile(s),
    each having three columns:  onset, duration, and weight.
  par -
    outputlocation should be a file, which will have four columns: onset,
    condition index, duration, and condition name.  The conditions will be
    numbered from zero (0), in the order they are specified in the query file.


Options:
  --overwrite
        Overwrite existing output files (otherwise error and exit).
  --bypass
        Missing files or other errors will result in warning messages but
        processing on other files will continue, and the exit status will
        be 0 (success).
  --verbose
        Provide more info for debugging.
  --tr TR
        Specify the TR.  Equivalent to specifying "forcetr" in the query file.
        This is used to convert "ptsbefore" and "ptsafter" options into seconds.
  --fileprefix PREFIX
        Except for outputformat 'par', output file names will have this prefix.
        Default is no prefix.
  --weightquery STRING
        If specified (and if supported by the output type) the weight for an
        event is 1 if this query matches on the event, and 0 otherwise.
        If neither --weightquery or --weightvaluequery is specified, the
        default weight is 1 for all events.
  --weightvaluequery STRING
        If specified (and if supported by the output type) the weight for an
        event is given by the value matching this query on each event, and the
        weight is zero for any event where this query does not match a value.
        If neither --weightquery or --weightvaluequery is specified, the
        default weight is 1 for all events.

Usage:
  ximg2bxh [opts] [ximgfiles...] output.bxh

This program creates an XML wrapper for GE Ximg image files.

  --dimzsize <size_t>
  --dimzsize=<size_t>
        Specifies the size of the z dimension (i.e. number of slices per
        timepoint).  Default is to use the number of input files.  Equivalent
        to (and overrides) --hintsizez.
  --dimtsize <size_t>
  --dimtsize=<size_t>
        Specifies the size of the t dimension (i.e. number of timepoints).
        Default is number of input files divided by number of slices per
        timepoint (as specified by --dimzsize).  Equivalent to (and overrides)
        --hintsizet.
  --inputsfromfile <str>
  --inputsfromfile=<str>
        Read list of input files from this file.
  --version
        Print version string and exit.
  --hintsizex <size_t>
  --hintsizex=<size_t>
  --hintsizey <size_t>
  --hintsizey=<size_t>
  --hintsizez <size_t>
  --hintsizez=<size_t>
  --hintsizet <size_t>
  --hintsizet=<size_t>
  --hintoriginx <double>
  --hintoriginx=<double>
  --hintoriginy <double>
  --hintoriginy=<double>
  --hintoriginz <double>
  --hintoriginz=<double>
  --hintorigint <double>
  --hintorigint=<double>
  --hintspacingx <double>
  --hintspacingx=<double>
  --hintspacingy <double>
  --hintspacingy=<double>
  --hintspacingz <double>
  --hintspacingz=<double>
  --hintspacingt <double>
  --hintspacingt=<double>
  --hintgapx <double>
  --hintgapx=<double>
  --hintgapy <double>
  --hintgapy=<double>
  --hintgapz <double>
  --hintgapz=<double>
  --hintgapt <double>
  --hintgapt=<double>
        These options will provide a hint to the program of the 'size',
        'origin', 'spacing', or 'gap' of the specified dimension.  Some image
        types will not use all these values.  In particular, sizex and sizey
        are assumed correct in most image headers, but they, as well as sizez
        and sizet options may be useful with image type 'pfile'.  Origin and
        spacing hints will be used by most image types.  
  --forceorientation <str>
  --forceorientation=<str>
        This option will force the labeled orientation of the image to match
        the given three letter orientation code.  Each letter must come from
        the following groups in any order: R(ight) or L(eft); A(nterior) or
        P(osterior); S(uperior) or I(nferior).  Only one letter from each group
        is allowed.
  --xcede
        Write XCEDE-style XML files.
  --xcede2
        Write XCEDE 2-style XML files.

Usage:
  fmriqa_volmeasures [opts] xmlfile

This program calculates various measures per volume of the input 4-D time
series, such as mean/minimum/maximum intensity, standard deviation, and
center-of-mass in all three dimensions.  The input file must be BXH or XCEDE
file, and the output will be written to standard output.

  --version
        Print version string and exit.
  --maskfile <str>
  --maskfile=<str>
        Use this mask (should be a BXH or XCEDE XML file).
  --timeselect <str>
  --timeselect=<str>
        Comma-separated list of timepoints to use (first timepoint is 0).  Any
        timepoint can be a contiguous range, specified as two numbers separated
        by a colon, i.e. 'START:END'.  An empty END implies the last timepoint.
        The default step of 1 (one) in ranges can be changed using
        'START:STEP:END', which is equivalent to
        'START,START+STEP,START+(2*STEP),...,END'.
  --xselect <str>
  --xselect=<str>
        Just like timeselect, but for the 'x' dimension.
  --yselect <str>
  --yselect=<str>
        Just like timeselect, but for the 'y' dimension.
  --zselect <str>
  --zselect=<str>
        Just like timeselect, but for the 'z' dimension.