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Hi Rosalia, I have everything is native space. INPUT and ROIs are already aligned but my goal is to convert INPUT and ROIs to align with REFERENCE file I have. Please let me know if this clarifies the issues I am having. I would be more than happy to send you these files if you need them to figure out the issue. Thanks, Sahil On Wed, Jan 20, 2016 at 10:25 AM, Rosalia Dacosta Aguayo < [log in to unmask]> wrote: > 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 >> >> -- >> ------------------------------------------------- >> 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] <[log in to unmask]> >> > > -- ------------------------------------------------- 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] <[log in to unmask]>