That will be in a future version of flirt, I didn’t realize it hadn’t been released yet.

 

You can ignore it for any flirt command you don’t care about the blurring of the output (i.e. you are just calculating the transformation matrix).  You can use applywarp to apply a transformation matrix with spline interpolation.

 

applywarp --interp=spline -i T2_brain.nii.gz -r T1_brain.nii.gz --premat=T2_to_T1.mat -o T2_to_T1.nii.gz will apply a precalculated transformation matrix (that you calculated earlier from flirt) to an image with spline interpolation. 

 

Peace,

 

Matt.

 

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From: Rosalia Dacosta [mailto:[log in to unmask]]
Sent: Tuesday, May 22, 2012 1:09 AM
To: FSL - FMRIB's Software Library; Matt Glasser
Subject: A problem with flirt

 

Hi Matt,

Yesterday I was trying the following command: flirt -interp spline -in T2_brain.nii.gz -ref T1_brain.nii.gz -omat T2_to_T1.mat -out T2_to_T1.nii.gz

But it does not work, because there is not interp spline option for flirt, the only options are:

-interp {trilinear,nearestneighbour,sinc}

Could you tell how can I change this in order to get the results?

Many thanks.

Rosalia.