Hi Bastian Hmm, if everything looks right when you view things inside FreeSurfer then it is goiong to be hard for us to help you as the issue sounds like it is a 3D slicer one. Have you contacted them? You can use mri_info to look at the headers and the ras2vox matrices. Typically this is a problem of where the center of the coordinate system is (frequently called c_ras - the RAS coordinates of the center of the volume).
cheers Bruce On Mon, 24 Oct 2016, Conrad Christoffer Prillwitz wrote: > Dear Freesurfer-Expert, > > I'm very sorry for reposting this issue again, but we are really in the need > of help as we ourselves do not find any solution to this problem. > We would be very grateful for any hint related to this. > > We are currently trying to develop a 3D-Model from MRI data using combined > files from Freesurfer and FSL. For this purpose we run recon-all on our > subject and furthermore get some ROIs from FSL-based scripts. When > visualizing the Freesurfer surfaces together with the FSL ROIs in any 3D > modelling software (like e.g. Meshlab or 3D Slicer), there seems to be a > space mismatch meaning: the FSL-based ROIs lie more inferior relative to the > Freesurfer surfaces than they should (a shift in any other direction might be > there but is at least not visible by eye; see attached screenshot). If we > further add a single 2D slice of the original T1.mgz file to the 3D model, it > seems to be consistent with the spatial position of the FSL ROIs, while the > Freesurfer surfaces are clearly shifted (at least in z-direction; see > attached screenshot). However opening the surfaces and the T1.mgz in freeview > instead of 3D-Slicer, the spatial position fits. > > Do you have any idea of why this is the case or even more important, how to > bring both structures in the same "space"? As we need to continue modelling > in 3D-Slicer, we are looking for a way to correct the spatial shift > independent of freeview. > We are very thankful for any input on this matter! > > Best regards, > Bastian David > > > Bastian David, M.Sc. > Ph.D. candidate > .............................................................. > Department of Epileptology > University of Bonn > .............................................................. > Sigmund-Freud-Str. 25 > 53127 Bonn > .............................................................. > bastian.da...@ukb.uni-bonn.de > www.epileptologie-bonn.de _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
