Hello,
I am having trouble with convertwarp. I have a linear (FLIRT) and non-linear (FNIRT) warp that both work independently, but when I combine them with convertwarp the warp no longer works.
Here is my code:
convertwarp -o /home/andrew/mrtrix/subjects/eb$n/eb$n.fs2fa_warp.nii -r /home/andrew/mrtrix/subjects/eb$n/eb$n.FA.nii -m /home/andrew/mrtrix/subjects/eb$n/eb$n.fs2struct.mat -w /home/andrew/mrtrix/subjects/eb$n/eb$n.struct2fa_warp.nii
when I run the following code, the image is quite distorted:
applywarp -i /home/andrew/mrtrix/subjects/eb$n/eb$n.brain.nii -o /home/andrew/mrtrix/subjects/eb$n/eb$n.fs2faImg -r /home/andrew/mrtrix/subjects/eb$n/eb$n.FA.nii -w /home/andrew/mrtrix/subjects/eb$n/eb$n.fs2fa_warp.nii
However, when I first run:
#flirt -applyxfm -init /home/andrew/mrtrix/subjects/eb$n/eb$n.fs2struct.mat -in /home/andrew/mrtrix/subjects/eb$n/eb$n.brain.nii -ref /home/andrew/mrtrix/subjects/eb$n/eb$n.rawavg.nii -out /home/andrew/mrtrix/subjects/eb$n/eb$n.brain2raw.nii
and then run:
applywarp -i /home/andrew/mrtrix/subjects/eb$n/eb$n.brain2raw.nii -o /home/andrew/mrtrix/subjects/eb$n/eb$n.fs2faImg -r /home/andrew/mrtrix/subjects/eb$n/eb$n.FA.nii -w /home/andrew/mrtrix/subjects/eb$n/eb$n.struct2fa_warp.nii
the transformation works.
Any help would be appreciated.
Andrew
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