Flags in Load Varian
load_varian input_filename output_filename [-options]
- -ms
- Reorder data acquired in multislice.
- -epi
- Reorder data acquired using EPI, reversing alternate
echoes.
- -lpss n
- Reorder data acquired with the slice position (pss)
shifted every volume (looppss). The number of blocks that the
slices are split into is specified by n. The number of slices
divided by the number of blocks must be an integer. Must be used in
conjunction with the -epi flag.
- -fmap
- Reorder data acquired using the field mapping sequence
(spin-echo, asymmetric spin-echo pairs). Must be used in
conjunction with the -ms flag.
- -sear n
- Reorder data from a multislice experiment (with
seqcon='ncsnn') where a parameter has been arrayed. The number of
steps in the arrayed parameter is specified by n. Must be used in
conjunction with the -ms flag.
- -ft2d
- Perform a 2D Fourier Transform on a slice by slice basis
through the data series.
- -ft3d
- Perform a 3D Fourier Transform on each volume of the data
series.
- -ftr
- Fourier Transforms the rows only.
- -bl
- Correct the baseline offset.
- -zero n
- Zeropad each slice matrix to n x n.
- -zzero n
- Zeropad in the z (slice) direction to n. If the data
requires only 2D Fourier transformation then it is inverse Fourier
transformed in the z direction prior to zeropadding and then
transformed back.
- -rot
- Rotate each slice by 90 degrees.
- -negrot
- Rotate each slice by -90 degrees.
- -revproc
- Process the volumes in reverse order, but maintain the
original ordering in the output. This is useful if the last volume
in the series is a better estimate of those parameters taken from
the first volume only (e.g. scaling, self-reference phase
correction, phase rotation).
- -revload
- Process and output the volumes in reverse order.
- -hks
- Apply half-kspace (half-Fourier) processing. There are a
number of other flags that can control the type of half-kspace
processing options used, but these are intended for development and
testing.
- -hkspad
- Process the data as half-kspace, but without the
phasing or conjugation.
- -nav n/m/p/mp
- Signifies that the data has been acquired with
navigator echoes. Follow -nav with n to remove the navigator echoes
but do no processing with them. Specify m or p to use the navigator
to correct magnitude or phase of the data respectively and mp to
correct both magnitude and phase. Note that this is for EPI data
only and is in development.
- -shift n
- Shift the data array by n pixels (tep correction).
Note that n must be an integer.
- -start n
- Ignore the first n volumes.
- -num n
- Process n volumes only.
- -avwin
- Input file is a complex AVW file of time data.
- -raw x y z v
- Input file contains raw time data in the form of
real-imaginary pairs of short integers (shorts). The matrix
dimensions are specified in x,y,z and v.
- -series
- Process all images in a series. For example if the
input filename is series_3.1 then files
series_3.1.fid, series_3.2.fid,
series_3.3.fid etc. will be processed.
- -orig
- Read the raw data from the file
input_filename.fid/fid.orig instead of
input_filename.fid/fid.
- -ne n
- Specifies the number of echoes in a multi-echo data set.
This is only necessary if the number of echoes (ne) in procpar is
not correct.
- -16
- Output the data as 16-bit integers (shorts). The data will
automatically by scaled such that the maximum (0.99 percentile) is
20000.
- -mod
- Output the modulus of the complex data.
- -phs
- Output the phase of the complex data.
- -re
- Output the real part of the complex data.
- -im
- Output the imaginary part of the complex data.
- -resl
- Reslice the output data to the axial plane.
- -segx low num
- Segment the output volume in the x direction
starting from low, for num points.
- -segy low num
- Segment the output volume in the y direction
starting from low, for num points.
- -segz low num
- Segment the output volume in the z direction
starting from low, for num points.
- -cp fn
- Duplicates the output to this filename (fn).
- -ref fn
- The name (fn) of a reference scan to use in the
phase correction. In the absence of either -buo or -hu flags then
the reference scan is assumed to be a single volume EPI with no
phase-encoding.
- -buo
- Phase correction is done according to the Buonocore (self
reference) method. If no reference scan is supplied (the normal
case) then the first volume of the series is used to correct all the
data. If a reference scan file name is supplied (with the -ref
option) then this is taken to be a single phase-encoded volume from
which the phase correction will be calculated.
- -buov
- Apply the Buonocore correction (self reference)
correction on a volume by volume basis.
- -hu
- Phase correction is done according to the Hu method. This
requires the name of a phase-encoded reference scan (supplied with
the -ref option) with the phase-encoding of opposite polarity to the
main data.
- -con
- Constrains the phase correction to be a single linear
correction of alternate lines in the slice.
- -poly
- Constrains the phase correction to be a single fifth
order polynomial correction of alternate lines in the slice.
- -ph0 n
- Apply a zeroth order alternate line phase correction of
n.
- -ph1 n
- Apply a first order alternate line phase correction of
n.
- -scsl [fn]
- Scale slices in a volume based on slice position
and the scale values specified in a file
FSLDIR/tcl/rfcoil.scale or in the specified filename (fn).
- -scale n
- Scale all the values in the output data by a factor of
n.
- -max n
- Scale all the values in the output data so that the
maximum (based on 0.99 percentile) is equal to n.
- -kmb n
- Mask the border of each slice in k-space by n pixels
before Fourier Transform.
- -imb n
- Mask the border of each slice in the output image by n pixels.
- -phrot n
- Phase rotate volumes (in blocks of n) such that the
phase of the first volume in the block is zero across the whole
volume.
- -smod n
- Determine the sign of the phase of the data and output the
data as signed modulus. The data series is treated in blocks of n volumes.
- -phmap fn
- Apply a phase map to the output volume based on
the values in a complex AVW file (fn).
- -help
- View the help message.
- -overx n
- Force the x dimension in the header file to be n.
- -overy n
- Force the y dimension in the header file to be n.
- -overz n
- Force the z dimension in the header file to be n.
- -overv n
- Force the v dimension in the header file to be n.
Note that these values affect the output header file only and not
how the data is processed.
- -opss
- Extract the slice position array (pss) to a file named
output_filename.pss.