Thank Donna: I went through the segmentation tutorial and the videos, I think I understand where I should start.
Regards, Soha On Fri, Oct 9, 2009 at 9:23 AM, Donna Dierker <[email protected]> wrote: > 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 > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
