Hi Sahil,

It would be greatly appreciate if you could say in which space are the two images. I guess that one is in native space and the other is in MNI space...and I could gess as well that, regarding to your ROI you would like to go from MNI space to native space....what I can no only guess...so if you were a bit more concrete I could try my best to help you from what I have learned from FSL experts....

Yours sincerely,

Rosalia.

2016-01-20 16:52 GMT+01:00 Sahil Bajaj <[log in to unmask]>:

Dear FSL experts,

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

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Sahil Bajaj
Post-doctoral Fellow

Nantz National Alzheimer's Center, Department of Neurology

The Houston Methodist Research Institute (THMRI)

Houston, TX, USA.
E-mail:[log in to unmask]