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FSL  March 2008

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Subject:

Re: How to use FUGUE to correct distortion of EPI image?

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 17 Mar 2008 09:37:35 +0000

Content-Type:

text/plain

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text/plain (77 lines)

Dear Wang,

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
or
   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,
	Mark




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  
> data?
> 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  
> data?
>
> fugue -i epi --dwell=dwelltime --loadfmap=fieldmap -u result
>
> Should I substitute dwelltime with the total read out time of my EPI  
> data?
> 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  
> fieldmap?
>
> -s sigma
>
> Should I subsitute sigma with a number which used in 2D Gaussian  
> smoothing ,such as 0.5?
>
> --smooth3=sigma
> 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  
> respectively?
>
> fugue -i undistortedimage -p unwrappedphase -d dwelltoasymratio -s  
> 0.5 -w warpedimage
>
>  Should I substitute undistortedimage unwrappedphase  
> dwelltoasymratio and warpedimage with what?
>
> --mask=maskname
> Should I substitute maskname with the path and file name of pre- 
> defined mask data?
> --unwarpdir=dir
> Should I subsitute dir with one of x,y,z,x-,y-,z- (default is y)
> --phaseconj
> uses the phase conjugate correction method, rather than pixel shifts
> --nokspace
> for forward warping (only) - uses an image-space method for forward  
> warping
> --icorr
> applies an intensity correction term when using the pixel shift  
> method - often poorly conditioned for standard fieldmap acquisitions
> Thank you.
>
> Wang Qiang
>

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