AFNI program: ConvertDset

Usage: 
  ConvertDset -o_TYPE -input DSET [-i_TYPE] [-prefix OUT_PREF]
  Converts a surface dataset from one format to another.
  Mandatory parameters:
     -o_TYPE: TYPE of output datasets
              where TYPE is one of:
           niml_asc (or niml): for ASCII niml format.
           niml_bi:            for BINARY niml format.
           1D:                 for AFNI's 1D ascii format.
           1Dp:                like 1D but with no comments
                               or other 1D formatting gimmicks.
           1Dpt:               like 1Dp but transpose the output.
           gii:                GIFTI format default .
           gii_asc:            GIFTI format with ascii DataArrays.
           gii_b64:            GIFTI format with Base 64 encoded DataArrays.
           gii_b64gz:          GIFTI format with B64 enconding and gzipping.
         For stderr and stdout output use one of:
           1D_stderr, 1D_stdout, niml_stderr, or niml_stdout, 
           1Dp_stdout, 1Dp_stderr, 1Dpt_stdout, 1Dpt_stderr
         Actually, this parameter is not that mandatory, the program
         can look at extensions on the prefix to guess the output
         format. If the prefix has no extension and o_TYPE is not
         specified, then the output format is the same as that of the
         input.
     -input DSET: Input dataset to be converted.
                  See more on input datasets below.
  Optional parameters:
     -add_node_index: Add a node index element if one does not exist
                      in the input dset. With this option, the indexing
                      is assumed to be implicit (0,1,2,3.... for rows 0,1
                      2,3,...). If that is not the case, use -node_index_1D
                      option below. 
     -node_index_1D INDEX.1D: Specify file containing node indices
                              Use this to provide node indices with 
                              a .1D dset. In many cases for .1D data
                              this option is DSET.1D'[0]'
     -node_select_1D MASK.1D: Specify the nodes you want to keep in the
                              output.
     -prepend_node_index_1D: Add a node index column to the data, rather
                             than keep it as part of the metadata.
     -pad_to_node max_index: Output a full dset from node 0 
                            to node max_index (a total of 
                            max_index + 1 nodes). Nodes that
                            get no value from input DSET are
                            assigned a value of 0
                            Notice that padding get done at the
                            very end.

     -i_TYPE: TYPE of input datasets
              where TYPE is one of:
           niml: for niml data sets.
           1D:   for AFNI's 1D ascii format.
           dx: OpenDX format, expects to work on 1st
               object only.
           If no format is specified, the program will 
           guess using the extension first and the file
           content next. However the latter operation might 
           slow operations down considerably.
     -prefix OUT_PREF: Output prefix for data set.
                       Default is something based
                       on the input prefix.
  Notes:
     -This program will not overwrite pre-existing files.
     -The new data set is given a new idcode.

  SUMA dataset input options:
      -input DSET: Read DSET1 as input.
                   In programs accepting multiple input datasets
                   you can use -input DSET1 -input DSET2 or 
                   input DSET1 DSET2 ...
       NOTE: Selecting subsets of a dataset:
             Much like in AFNI, you can select subsets of a dataset
             by adding qualifiers to DSET.
           Append #SEL# to select certain nodes.
           Append [SEL] to select certain columns.
           Append {SEL} to select certain rows.
           The format of SEL is the same as in AFNI, see section:
           'INPUT DATASET NAMES' in 3dcalc -help for details.
           Append [i] to get the node index column from
                      a niml formatted dataset.
           *  SUMA does not preserve the selection order.
              For example:
              dset[44,10..20] is the same as dset[10..20,44]


 SUMA mask options:
      -n_mask INDEXMASK: Apply operations to nodes listed in
                            INDEXMASK  only. INDEXMASK is a 1D file.
      -b_mask BINARYMASK: Similar to -n_mask, except that the BINARYMASK
                          1D file contains 1 for nodes to filter and
                          0 for nodes to be ignored.
                          The number of rows in filter_binary_mask must be
                          equal to the number of nodes forming the
                          surface.
      -c_mask EXPR: Masking based on the result of EXPR. 
                    Use like afni's -cmask options. 
                    See explanation in 3dmaskdump -help 
                    and examples in output of 3dVol2Surf -help
      NOTE: Unless stated otherwise, if n_mask, b_mask and c_mask 
            are used simultaneously, the resultant mask is the intersection
            (AND operation) of all masks.


   [-novolreg|-noxform]: Ignore any Rotate, Volreg, Tagalign, 
                or WarpDrive transformations present in 
                the Surface Volume.
  Common Debugging Options:
   [-trace]: Turns on In/Out debug and Memory tracing.
             For speeding up the tracing log, I recommend 
             you redirect stdout to a file when using this option.
             For example, if you were running suma you would use:
             suma -spec lh.spec -sv ... > TraceFile
             This option replaces the old -iodbg and -memdbg.
   [-TRACE]: Turns on extreme tracing.
   [-nomall]: Turn off memory tracing.
   [-yesmall]: Turn on memory tracing (default).
  NOTE: For programs that output results to stdout
    (that is to your shell/screen), the debugging info
    might get mixed up with your results.
 

Examples:
1-   Plot a node's time series from a niml dataset:
     ConvertDset -input DemoSubj_EccCntavir.niml.dset'#5779#' \
                 -o_1D_stdout | 1dplot -nopush -stdin 

++ SUMA version 2006_7_3

CVS tag:
   SUMA_2005_04_29_1733

Compile Date:
   Jan 29 2009

    Ziad S. Saad SSCC/NIMH/NIH saadz@mail.nih.gov    Thu Apr  8 16:15:02 EDT 2004