Thank you Jan-Mathijs, I will consider your first and last suggestion. I don’t want to reinvent the wheel again. best tzvetan
> Hi Tzvetan, > > It sounds you want to do a beamformer type of source reconstruction using > source positions defined on a 3D grid. You could use the provided data for > this, where the individual grids are in register with a grid in normalised > volume. Assuming you are doing all in FieldTrip anyway, you could interpolate > the volumetric atlas onto one of the template grids (which are part of the > software release, but can also be found in FieldTrip), which will give you > the anatomical labelling for each of your beamformer’s dipole positions right > away. Alternatively, if you would really want to create your own 3D-grid, you > should plug in the appropriate transformation matrix from the transform > text-file into the anatomical MR-structure. A different route altogether, and > this is what the HC-consortium is pushing for, is to work in > surface-registered space. This does much more credit to the analysis of the > data from the haemodynamic and structural modalities. Although it’s still an > open question whether MEG in itself will benefit from a surface-based > analysis (when using beamformers), you could consider using the cortical > sheet source models, in combination with an anatomical labeling defined on > the surface (e.g. the Conte69 atlas). Of note, if you were working on the > surface, you could benefit from any cool parcellation schemes that may be > coming out of the consortium soon. > > Best wishes, > > Jan-Mathijs > > > On Apr 27, 2015, at 9:37 AM, Tzvetan Popov <[email protected]> wrote: > >> >> 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 >>>> >>> >> > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
