DESCRIPTION

The core rumba utilities perform basic file manipulation operations, operations on data, and allow inspection of data.

align

Utility for computing parameters to realign one data set with another. This program includes algorithms for affine, rigid body, and polynomial warps, and both intra-modality and inter-modality transforms.

babelfish

Conversion tool. Converts data between different formats. Supported formats include analyze, Siemens dicom, Siemens IMA, and Stimulate.

bin2txt

Dump a binary file to text. Useful for examining the contents of files containing binary data.

dicomcat

Utility to convert a dicom series into a single analyze file.

dicom2img

Utility to convert a dicom series into a series of analyze files.

dicomls

List all dicom series in a given directory.

dumpheader

Tool for displaying header information in a data set.

getheader

Tool for displaying individual headers in a data set.

getslice

Tool for extracting subsets of data. Any region m(x,y,z,t) where x,y,z,t all range over some interval may be used, so this tool can both extract slices and crop.

makeheader

Create an analyze header file.

manifoldcat

Create a 4d dataset from several 3d data sets, by appending them, or create a 3d data set by appending 2d datasets.

manifoldstat

Display summary statistical information (mean, standard deviation, sum of squares, voxel and spatial dimensions, histogram) of a data set.

manifolduncat

Break a 4D data set into multiple 3D data sets.

reslice

Resample a data set using a spatial transformation computed using the align program.

rumbaview

Software to view datasets.

txt2bin

Convert an ascii file to a binary file. Combined with makeheader, this program can be used to make "hand built" analyze format files.

AUTHOR

REPORTING BUGS

COPYRIGHT

Index

NAME

SUMMARY

DESCRIPTION

AUTHOR

REPORTING BUGS

COPYRIGHT

align

(-i|--infile) infile (-s|--standard) standardfile \
      [(-m|--mask) maskfile] [ (--rigid|-r)|(--affine|-a)|((--poly|-p) degree)] \
      [(--timebudget|-t) t]  [--cost|-c ratio|ls] [-o|--outfile] outfile

   outfile transformation
   infile ------------------------> standardFile

- looks for a transformation from 'infile' to 'standardfile' and saves resulting transformation into 'outfile'
- rigid transformation is default if none specified
- degree of polynomial transformation must be from 2 to 5
- cost is a cost function
- ratio is a similar cost function to that used by AIR, appropriate for between-modality affine registration.
  At present, it only works with affine registration (not rigid or polynomial). ls is the least squares cost
  function, and the default for this algorithm.

no help available

usage: bin2txt -i infile  [-z] [ -o outfile ]
      -z   to dump in format for each row: t x y z value

Usage: babelfish [-i|--infile] infile [-o|--outfile] outfile  [--be|--le]

Usage: dumpheader [-i|--infile] infile

Usage: getheader [-s] -i infile -o outfile header1 header2 header3

Usage: getslice -i infile -o outfile x y z t dx dy dz dt

Usage: makeheader -o outfile [ --type char|short|int|float|double ]
width height depth timepoints [--dimx d1] [--dimy d2] [--dimz d3] [--dimt d4]

Usage: manifoldcat [-h | -i infile1 infile2 infile3 ... -o outfile --sort [none|alpha|numeric|origin]] [--verbose|-v] [--simple]

Usage: manifolduncat [-h | -i infile -o outfile

reslice (-i|--infile) infile (-t|--transf) transformationfile \ (-n|--interp) XYZ \ [ (--extent|-e) x,y,z ] [ (--dims|-d) x,y,z ] \ [-o|--outfile] outfile transf infile (some extent, some dims)  --------> outfile (extent, dims)

Applies transformation parameters of which are provided in transformationfile and saves
result into 'outfile'.

If desired size (extent) or dimension sizes (dims) of output image are not provided -
they are assumed to be the same as of original image.
Polynomial transformation is default if none is specified

usage: rumbaview -i|--infile  [-y|--overlay ]
[-n|--normalize-vols] [-s|--stretch param] [-c|--colormap ] [-h|--help] [-v|--verbose]

  Options:
  -i, --infile     Input file
  -y, --overlay    Overlay file
  -n, --normalize_vols   Normalise the volumes
  -s, --stretch   Stretch volumes by 
  -c, --colormap   Read colormap from 
  -z, --zoom     Zoom images by 
  -h, --help             Display this help message
  -v, --verbose          Display verbose information

usage: talairachlabel [-i infile] [-o outfile] [-c|--show-coords]
                      [-t|--talairach] [-r|--relative-to-origin]
Get the brodman area information from the talairach atlas
for the coordinates from stdin or from an input file

-i                         Input file with coordinates
-o                         Outfile file to dump the output, otherwise stdout
-c, --show-coords          Show coordinates when outputing the brodmann areas
-t, --talairach            Coordinates are in talairach space (1x1x1mm)
			   otherwise assumes in mni space (2x2x2mm)
-r, --relative-to-origin   Coords are relative to the origin standard form
			   i.e., in spatial units (mm), otherwise the default
			   assumes raw voxel dimensions

Usage: txt2bin [ -i infile ] [ -o outfile ]         [ --type char|short|int|float|double ]

usage: mean_intime [-i infile] to compute the mean in time of the 4D volume