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Hi, Your REFERENCE file...is in native space as well or is in MNI space? Rosalia. 2016-01-20 17:44 GMT+01:00 Sahil Bajaj <[log in to unmask]>: > 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]> >