Hi Jan-Mathijs, > Hi Tzvetan, > > Which anatomical MR are you using? I’m using '100307_3T_T1w_MPR1.nii.gz’. > Note that the ‘baked in’ fiducial locations are indeed approximate, but they > only make sense in context of the anatomical image in which they have been > clicked. This image was a 1mm resolution image with a sufficient field of > view to capture the entire scalp surface + facial details. This image is not > part of the released data. Got it. Want work then indeed. I assumed that the approximate locations are based on the provided MRI. All clear. > Thus, in short, the fiducial locations (defined in voxels) don’t make sense > in the context of the anatomical image you are using. > Since everything is already in register (and the co-registration details are > represented in the 100307_MEG_anatomy_transform.txt), what is it you want to > do? Yes all is co-registred and I was able to do source analysis etc. What I wanted to do is to re-compute the sourcemodel warped in the aal-mni-space instead of mni-space as it is now. Many thanks tzvetan > > Best wishes, > > Jan-Mathijs > > > > Jan-Mathijs Schoffelen, MD PhD > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > [email protected] > Telephone: +31-24-3614793 > > http://www.hettaligebrein.nl > > > > > > > On Apr 27, 2015, at 8:08 AM, Tzvetan Popov <[email protected]> wrote: > >> Dear hcp-users, >> >> I am trying to coregister the individual MRI and the 4D coordinates using >> the fiducial information provided in ‘100307_MEG_anatomy_fiducials.txt’. >> When using the provided voxel coordinates the anatomical image is misaligned >> (see attached figure 2). Interactively providing the approximate coordinates >> of the fiducials aligned the volume correctly (attached figure 1). It >> appears to me that the provided voxel coordinates are somewhat off. . Am I >> doing something wrong, has anybody encountered similar problem? >> Thanks a bunch in advance >> tzvetan >> >> Here is the code snippet that will produce the two figures >> >> cfg=[]; >> cfg.method = 'fiducial'; >> cfg.fiducial.nas = [ 40 154 94 ];% hcp locations >> cfg.fiducial.lpa = [ 139 168 169 ];% hcp locations >> cfg.fiducial.rpa = [ 141 171 26 ];% hcp locations >> mriR = ft_volumerealign(cfg, mri); >> ft_determine_coordsys(mriR, 'interactive', 'no’); >> >> cfg=[]; >> cfg.method = 'fiducial'; >> cfg.fiducial.nas = [128 299 141 ];% my interactive locations >> cfg.fiducial.lpa = [ 240 148 91 ];% my interactive locations >> cfg.fiducial.rpa = [ 29 157 80];% my interactive locations >> mriR = ft_volumerealign(cfg, mri); >> ft_determine_coordsys(mriR, 'interactive', 'no'); >> >> >> <Misaligned.png><Aligned correctly.png> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >
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