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fScan Reference Manual, Chapter 2 (CmdLineOptions): header

Header -- Output file format specifications

usage: -header options

The HEADER command controls various data set formatting options. The command modifies the output data set if the -output command has been specified, otherwise the -header options modify the current active (input) data set.

The HEADER command options can be used to specify file formats and to specify the order in which output data are written to disk files.

  • FORMAT - Normally the input data format is detected automatically based on the filename or looking at the first few bytes of the file. The output file format is set by default to the format named in the global environment variable OUTFORMAT (which can be set to one of the output formats listed below.) The default format for saving images is XML (.IMG files with a .BXH XML header). Adding a .HDR header with the same name will allow the same .IMG file to be read as Analyze or NIFTI format as well. The default output format for making screenshots of interactively displayed windows (using the SNAPSHOT command) is JPEG format. These defaults can be overridden by explicitly by using the SET command to change the value of FSCANOUTFORMAT, or by using the HEADER command specifying the FORMAT argument to be one of the following character strings:
  • analyze - XYZ volumes with ANALYZE (168 byte) headers (1 XYZ series/file)
  • volumes - XYZ volumes without header (1 XYZ series/file)
  • pfile - GE k-space raw data
  • dicom - DICOM image format
  • bxh - Duke's BIAC XML header
  • nifti - NIFTI version of ANALYZE (1 XYZ series/file)
  • dmod - Pittsburgh MR Ctr file format (default)
  • pmri - Pittsburgh MRI format
  • bshorts -
  • bfloats -
  • cor -
  • surface -
  • tiff -
  • jpeg -
  • genesis - images in GE's GENESIS format
  • epirt - GE's epiRT pulse sequence data
  • epiduke - Duke's custom EPI pulse sequence data
  • apd2 - ANMR's APD2 image format
  • spiral - Duke's custom spiral pulse sequence data
  • mrgray - data file will have header appropriate for 'mrGray' software (Wandell et al.). NOTE: for mrGray the output should be in bytes
  • raw - raw MR data

Additional file formatting options can be specified for output files by including the following flags:

  • 2files - put header and data in 2 separate files (default if no args)
  • dataonly - write output data file only, no header
  • allhdrs - save header from every image in header file (assumes 2files
  • hdronly - a new header file is created, which points to the datain the input file
  • flipx - flip data along the X axis
  • flipy - flip data along the Y axis
  • flipz - flip data along the Z axis
  • flipt - flip data along the time axis
  • flipx - flip data along the X axis
  • rotate90cw - rotate images 90 degrees clockwise
  • rotate90ccw - rotate images 90 degrees counterclockwise
  • rotate90cw - rotate images 180 degrees

See Also:

fScan Home,
fScan Manual,
Manual Help

jvs/fscan/manual/chapter2/header.txt · Last modified: 2020/01/30 18:12 by voyvodic