Yes, you should substitute all these things.
A typical line might look _something_ like:
fugue -i /home/mark/study2/epi -p /home/mark/study2/uphase -d 0.32 -
s 0.5 -u /home/mark/study2/epi_unw
fugue -i /home/mark/study2/epi --dwell=0.000762 --loadfmap=/home/
mark/study2/fmap -u /home/mark/study2/epi_unw
Hope this helps.
All the best,
On 11 Mar 2008, at 13:34, qiang wang wrote:
> I am a beginner of FUGUE. Although there ar some command lines in
> the manual of FUGUE EPI UNWARPING. But I do not know Liniux at
> all. .So I do not how to use FUGUE command lines.
> For example
> fugue -i epi -p unwrappedphase -d dwelltoasymratio -s 0.5 -u result
> Should I substitute unwrappedphase with the path and file name of my
> Should I substitute dwelltoasymratio with the total read out time of
> my EPI data?
> Should I substitute result with the path and file name of processed
> fugue -i epi --dwell=dwelltime --loadfmap=fieldmap -u result
> Should I substitute dwelltime with the total read out time of my EPI
> Should I substitute fieldmap with the path and file name of my
> fieldmap data?
> Should I subsititute result with the path and file name of processed
> -s sigma
> Should I subsitute sigma with a number which used in 2D Gaussian
> smoothing ,such as 0.5?
> Should I subsitute sigma with a number which used in 3D Gaussian
> smoothing ?
> -m 2D median filtering --poly=n 3D Polynomial fitting of degree n
> --fourier=n 3D Sinusoidal fitting of degree n
> Should I substitute m, n of above command lines with a number
> fugue -i undistortedimage -p unwrappedphase -d dwelltoasymratio -s
> 0.5 -w warpedimage
> Should I substitute undistortedimage unwrappedphase
> dwelltoasymratio and warpedimage with what?
> Should I substitute maskname with the path and file name of pre-
> defined mask data?
> Should I subsitute dir with one of x,y,z,x-,y-,z- (default is y)
> uses the phase conjugate correction method, rather than pixel shifts
> for forward warping (only) - uses an image-space method for forward
> applies an intensity correction term when using the pixel shift
> method - often poorly conditioned for standard fieldmap acquisitions
> Thank you.
> Wang Qiang