Hi,

I followed your suggestion to use applywarp, but got an error.

The following command was given:

applywarp -i invol -o outvol -r refvol --premat flirt_output.mat --interp spline,

where flirt_output.mat is the matrix produced by flirt to register invol to refvol.

The error message I got was:

--premat: Missing non-optional argument!

Can you advice me on a correct usage of applywarp in case of a
known transformation matrix.

Cheers,
Ed

On 14 Mar 2012, at 10:41, Stephen Smith wrote:

Hi - also, MJ has noted that it would be wise to take the abs() of the output if you use higher-order interpolation, just to make sure that all output is positive.
This is easy with fslmaths.

Also, if you wanted faster sinc-like interpolation, you could use the spline option via a call to applywarp (fed from the FLIRT-output transform).

Cheers.


On 14 Mar 2012, at 08:04, Stephen Smith wrote:
Hi - we've discussed this and think we probably agree with you that sinc may be better.

Cheers.

On 14 Mar 2012, at 07:47, Ed Gronenschild wrote:
Hi,

Eddy_correct uses flirt for registration to the reference volume.
By default the final interpolation method is trilinear. I have
used sinc by using the options -sinc -sincwindow hanning.
The result looks more crispy, less blurred, as expected. My question is:
is there any fundamental objection against using sinc interpolation
in the eddy current correction?

Regards,
Ed