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OK - can you compare the header of the ROI and the standard space image? I know at some point in the past we had issues with ROIs generated in FSLView getting saved with headers that caused similar problems, but I thought this was fixed in the latest version of FSL. Are you running the latest patch release? Cheers. On 17 Sep 2009, at 05:35, Vinod wrote: > Hi Steve, > > I have tried that and that seems to work fine. > > Vinod > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > Behalf > Of Steve Smith > Sent: Thursday, September 17, 2009 12:12 AM > To: [log in to unmask] > Subject: Re: [FSL] Registering ROI from standard to subject space > > Hi - your command looks correct - what happens if you apply this > backwards transform to the standard space image instead of the ROI - > does that work? > Cheers. > > > On 16 Sep 2009, at 23:49, Vinod Venkatraman wrote: > >> Hi, >> >> I am trying to register an ROI created in standard space to >> individual subject space and find that they are considerably >> displaced. As an illustration, I have defined a random ROI around >> then ventricles on the standard image. I then used the following >> command to transform it to subject space (based on the parameters >> from earlier first level registration). >> >> Flirt -in roi_standard.nii.gz -ref example_func.nii.gz -applyxfm - >> init standard2example_func.mat -out roi_subject.nii.gz. >> >> I have attached the original ROI overlay on standard image and the >> transformed overlay on the subject's example_func image. As you can >> see, the transformed ROI is considerably displaced. Any ideas what I >> may be doing wrong here? The original registrations at the first >> level look fine. >> >> Thanks >> Vinod >> >> PS: I have also applied flirt as a two stage process going from >> standard to highres and then from highres to functional and results >> look the same. >> >> <roi_subject.png><roi_standard.png> > > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > --------------------------------------------------------------------------- > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------