what is your command line? I think there is a rescaling in which it expcts the phase to be 0-2048 (or 4096) as this is how it comes of the (siemens) scanner. Could that be the problem?


On 2/10/16 10:40 PM, Joseph Dien wrote:
I ran into the same issue:

FSLVersion 5.0.4
FSLVerMaj 5
FSL Version is 5.0.4, must be 3.X or 4.X

I downloaded the epidewarp.fsl script from the suggested ftp site and replaced the existing script.  It did indeed fix the version incompatibility with FSL 5.x.

I ran into a new problem where it was aborting.  After some trouble shooting and looking over the documentation, I realized that —-epi is a required input without which the script crashes (or is it supposed to be optional but there is a bug in the script?).

After including it, it ran much further but then aborted with the following error:

ERROR: input phase image exceeds allowable phase range.
Allowable range is 6.283 radians.  Image range is: 12.5633 radians.

This is consistent with the documentation.  I’m not sure why the phase image exceeds the range though.

It ran without problems with SPM’s FieldMap Toolbox and it is from a standard Siemen’s scanner sequence (two magnitude files and one phase difference file).

Do I just divide the values by two with something like fslmaths since it seems to have exactly double the required range?

Joe

On Nov 26, 2014, at 21:36, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:


It is there again. I don't know what the status if it  is in terms of the version. Try it and let me know
doug

On 11/25/14 4:34 PM, Morgan Hough wrote:
Hi Doug,

Could you put the epidewarp.fsl script back on your ftp site? I don’t see it at the link in the archives:


BTW, is the script updated in some way for 5.x or can I can the old script just be changed to accept 5.x version numbers. 

Cheers,

-Morgan

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