Hi Soha, Just double-checking: It sounds like you don't have a surface yet. You want to generate one. Go here:
http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Segmentation If your volume isn't already in NIfTI format, see if you can write it out that way, so you don't have to sweat the origin and orientation. If your origin isn't near the AC, then you'll need to save a version of your volume with the origin near the AC. Save both whole brain volumes -- before and after origin tweaking, so it will be easy to compute the translation between them. We typically spatially normalize our data with an affine transform before segmenting it, for reasons given here: http://brainvis.wustl.edu/help/why_normalize_input/ But there are lots of ways to do things; there is no best way for everyone. Donna On 10/08/2009 03:13 PM, soha saleh wrote: > Thank you. But I do not have the surface ready in caret topo/coord > form to start with, how to start by using mri hi-res images. > > thanks again! > > Soha > > On Thu, Oct 8, 2009 at 2:28 PM, Donna Dierker > <[email protected] <mailto:[email protected]>> wrote: > > On 10/08/2009 11:01 AM, soha saleh wrote: > > Hi Donna and caret users: > > > > I need to map the functional MRI data onto reconstructed surface of > > our subject's MRI data. Can we do this using caret? If yes > please give > > me some help with that. > Yes: > > If the surface is already in Caret .coord/.topo form, then you can go > straight here: > > > http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MapVolumeToSurface > > If the surface is in Freesurfer format, you can import it using > the GUI > using File: Open Data File: FreeSurfer Binary Surface File; however, > you'll probably find it easier to use one of the scripts out there for > importing Freesurfer surfaces. Here is one such script: > > > http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2009_09/freesurfer2caret.Ver2a.preborder.mni2wustl.sh > login pub > password download > > But certain steps are study-specific (e.g., the appropriate affine > transforms to apply to the surface, which depends on input). > > > > I guess this is doable using FreeSurfer, but I never used FreeSurfer > > and I am a new Caret user, if it is doable in both, which is better > > and easier?! > I'm certain Freesurfer can map functional data onto Freesurfer > surfaces, > but I don't know how to do it. Nor do I know which is better. > > For mapping in Caret, we typically use the midthickness surface as the > mapping substrate. The most popular mapping algorithms are enclosing > voxel and interpolated voxel. The web page above explains the > algorithms. > > > > Thank you! > > > > Regards, > > Soha > _______________________________________________ > caret-users mailing list > [email protected] <mailto:[email protected]> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ------------------------------------------------------------------------ > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
