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Dear Mark and all,

    Thanks again for your keeping me informed. Now I want to know how
to prepare input 4D image.

    I tried in the last hours and failed to get  a result.

    As you know the command line of eddy current correction is as
follows.

           eddy_correct <4dinput> <4doutput> <reference_no>

   But I met troubles in preparing 2D input images.  Does anyone know
how to convert a series of dicom images to 4D images which FSL required?
 Is there a file which introduce in detail the usage of eddy_correct?

   Thanks.

All the best.

J.




>>> Mark Jenkinson <[log in to unmask]> 02/13/07 4:53 PM >>>
Dear Jiali,

There is a tool called eddy_correct which you can run
either from the command line or from the FDT gui.
I recommend you use that.

All the best,
	Mark


On 13 Feb 2007, at 21:04, Jiali Cui wrote:

> Hi, everyone,
>
>      Actually, I mainly want to known the usage of flirt when it is
> applied  to eddy current correction.
>
>      Thank you very much.
>
> Best
> J.
>
>
>>>> Jiali Cui <[log in to unmask]> 02/13/07 12:23 PM >>>
> Hi, everyone,
>
>     I have THREE questions about FSL flirt. Would some guy can help
me
> with this? Thanks.
>
>     (1)  I found negative values in the results when I use FSL
flirt.
> Does anyone know why?
>
>          My experiments includes the following steps.
>
>          First, I use the flirt package to do image coregistration.
> the
> command line is shown as follows.
>
>        flirt  -in inslice.hdr  -ref refslice.hdr -out outslice 
-omat
> omat.txt  -2D
>
>          Then I used NII package to see the results named
> outslice.nii,
> and found negative values.  Why?
>
>    (2) How to use flirt to correct distortion induced by eddy
current?
>
>    (3) Is there any good tools to read and write nii format images?
>
> Thanks a lot.
>
> J.
>
> Best Wishes
>