EPI  Reconstruction (epirecon_ex)

Changes from the original epirecon:
  1. Added the ability to write directly to AFNI, Analyze, and Interfile file formats
  2. The scale factor given on the command line is now a linear scale factor rather than an inverse-square scale factor. If this argument is not given a scale factor is automatically computed as described in the next comment.
  3. The program now buffers frames of data in groups of 50. The scale factor is computed over the first buffer that is reconstructed. If method 0 is specified (see below), the scale factor is calculated as the quantity that will yield a maximum value of 26000. If method 1 is specified, it is computed such that the mode (histogram peak) of the voxels in the brain will be equal to 10000. The second method is less sensitive to outliers. Note that this is a multiplicative scale factor, and that processing with the general linear model will only correct for additive errors, so there is some benefit to scaling data in each run to the same value.
  4. The ref.dat file is now assumed to be in either the current working directory or in the same directory as the data. This simplifies scripting.
  5. Printouts to the screen are reduced although everything is still dumped to the log file.
  6. The version number and compile date are written to each log file.

epirecon_ex -f <raw data filename> [Options]

  • -H, -F Hammming filter or Fermi Filter
  • -skip nskip: [# images to skip in stimulate file (4 default)]
  • -ZX xdim: Zero fill X dimension to xdim (nfill must be power of 2)
  • -ZY ydim: Zero fill Y dimension to ydim (nfill must be power of 2)]
  • -NBP [Don't apply BP Asymmetry Correction (Default = ON)]
  • -NAME name: The output file name is given <dir>/<stem>.<ext> where dir and stem are derived from 'name' and 'ext' is appropriate for the chosen file format.
  • -reps n: Reconstruct 'n' frames
  • -scale scale_factor: Linear scale factor to overide autoscale feature.
  • -scltype method: How to compute scale factor. If method=0, it is calculated as 26000/max. If method=1, it is calculated as the 10000/median where the median is computed over voxels inside the brain.
  • -fmt: Output image format. Takes on values of ana, brik, sdt,
  • fni, and ifh. The default format is 'brik'
  • ana: Analyze format. (multiple 3D images)
  • ana4: Analyze format (one 4D image)
  • brik: AFNI format.
  • sdt: Stimulate format
  • fni: GE I.00n format
  • ifh: Interfile format (Flat floating point file w/ ASCII header.
  • -ksp: Save k-space data for the first frame. (to KS2*).
  • -DEBUG: Print even more useless information.
Environment Variables:
  • EPIRECON_PATH specifies the path to calibration files.
    • The path is set to "./" if EPIRECON_PATH is undefined.
    • Calibration files appropriate to the data being reconstructed are used if EPIRECON_PATH=default ( theprogram will choose from /apps/reconstruction/epirecon_calibration_files/3Tcalfiles/2003.01.09/ESE_* depending on the version of the P file.)
    • AFNI_PLUGINPATH must be set to the path of "to3d" to write to AFNI format files. (/apps/linux/afni-2.56/linux_gcc32)
  • The program was compiled on ancho (gcc 3.3.1) and will run on ancho, chilaca, mirasol, mulato, pasilla, and poblano.
  • Last modified February 24, 2011

    Last modified February 24, 2011