Hi,
I have an issue in using flirt command for FSL (5.0). I used flirt and it works well to co-register an image, say INPUT using REFERENCE and get final co-registered image as OUTPUT and transformation matrix OUTPUT.mat.
Now I have ROIs defined in the INPUT image space, so I tried to transform these ROIs into OUTPUT image space using OUTPUT.mat matrix using following command:
flirt -in ROI.nii -ref REFERENCE.nii -applyxfm -init OUTPUT.mat -out NewROI.nii
But I get following error after I run this:
terminate called after throwing an instance of 'NEWMAT::SingularException'
Aborted (core dumped)
I would really appreciate if someone could help me in figuring this out ?
Thanks,
Sahil
Hi, it might be useful to some one.
I just found that this is an issue which affects older versions of FSL. I think it has been fixed in the latest release (5.0.9).
Thanks to Paul Mccarthy.
Yes. I have never faced this problem with the latest FSL version in Linux.
Why don't you try FSL interface instead of the command line to c if the problem remains?
In the command u have entered some elements are missing, see below. U need to choose what interpolation u want to apply!
flirt -in ROI.nii -applyxfm -init OUTPUT.mat -out NewROI.nii -paddingsize 0.0 -interp trilinear -ref REFERENCE.nii
Also check if u don't have any spaces or special characters in ur files names!
Hi Salem, thanks a lot for the suggestions. Actually I have figured that out, it was all just because of older version of MATLAB.
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