User Tools

Site Tools


jvs:fscan:manual:chapter2:output

fScan Reference Manual, Chapter 2 (CmdLineOptions): output ===== Output – =
====
usage: -output [formatname] filename [flag]
or: -output [wordsize] filename [flag]
or: -output > stdoutfile
or: -output » stdoutfile
or: -output stdout 0

If FILENAME is “prompt”, you will be asked to enter a filename interactively.

FORMATNAME indicates what type of output file to create. The recognized options are:

  • biac – images with BIAC's BXH header
  • analyze – images with Analyze headers
  • jpeg – images in JPEG format
  • tiff – images in TIFF format
  • dicom – images in DICOM format
  • pfile – images in GE raw k-space “p-file” format
  • signa – images in GE “IMGF” format
  • volumes – images in BIAC volume format (no header)
  • bshorts – images in FreeSurfer's “bshort” format
  • bfloats – images in FreeSurfer's “bfloats” format
  • cors – images in FreeSurfer's coronal “cor” format
  • dmod – images in UPMC's “DMOD” format (obsolete)
  • imgf – images in GE “IMGF” format
  • nifti – images in NiFTI format
  • mgh – images in MGH format
  • xml – same as BIAC
  • pdigm – behavioral data
  • surface – surface data (vertices and triangles)
  • paint – surface index data in FreeSurfer format
  • curv – surface index data in FreeSurfer format
  • wdf – Workspace definition XML file
  • wsf – Multiple workspace XML file
  • hdronly – only create header file(s) that point to existing data file(s)
  • subject
  • zip
  • matrix

The FLAG argument can be used to specify additional options when writing out files.
FLAG values when writing image files:
* 020 - if in active display mode, flip images using display FLIPFLAG flags
* 020 - if no window display, flip images using HEADER flip flags (not working yet)

FLAG values when writing 3D surface files:
* 020 - include all surfaces (default is just first active surface)

FLAG values when writing workspace (WDF or WSF) files:
* 010 - do not write in XML format
* 020 - include all data sets (default is only to include only open data sets)
* 040 - do not include alignment matrices (written by default if there is alignment)
* 01000 - when writing WDF, include data sets from both workspaces (default is only current workspace)

The OUTPUT command can also be used to redirect standard output (stdout) to a file, causing text that would normally be displayed on the screen to be sent to that file.

To redirect text output to a new file, use:
-output > filename
To append text output to a file, use:
-output » filename
To stop redirecting output, use:
-output stdout 0

Note: If using the OUTPUT command to redirect output from a shell command line you must escape each '>' character with a '\' (e.g. “-output \>\> outfile.txt”) to prevent the shell from misinterpreting the redirection.

See Also:
FLIPFLAG,
HEADER

fScan Home,
fScan Manual,
CmdLineOptions,
Manual Help

jvs/fscan/manual/chapter2/output.txt · Last modified: 2020/01/30 17:01 by voyvodic