> Ya, sorry for the incomplete query. Our interest is to view and threshold fMRI/voxel correlation data over the fiducial brain surface created out of high res image of individual macaques. 1. we used CARET 5.65 for creating the fiducial surfaces(following the caret5 tutorial guide for segmentation).we used individual already coregistered high res images for this purpose. 2. then we tried overlaying the fMRI data(spmT file from analysis using spm8) on the fiducial surface (following the procedures from http://prefrontal.org/blog/2009/04/using-caret-for-fmri-visualization/ and the tutorial guides).
we ended up having a) fiducial surfaces with fmri data mapped onto it. But the voxel coordinates did not match properly with the results in spm8. I should tell you one thing that we found: when we overlay whole brain fmri results, it matches more or less in x&y axes but not in z axis. and when we overlay results from explicitly masked analysis(roi), it seems to be shifted caudally by 2-3mm in R-C axis. same things when checked in spm8, shows up to be well coregistered! b)Another issue is we are not able to threshold the caret brain overlays in concordance with the thresholds that we use in spm. The metric thresholding range (user defined) doesn't seems to represent what we really need. eg:we tried overlaying FDR corrected voel corrln values, thresh 0.4 on the brain in caet and tried a range of metric thresholds(user scale 0-1, put display mode-pos,thresh type -user, tried changing user pos thresh values to 0.4 and voxels doesn't show up! Thank you donna, What software was used to reconstruct the surface? > > With freesurfer, there is an offset between the orig.mgz and the surface. > And depending on many factors, you might have to flip/rotate the surface > to be in the same orientation as the volume (or bring the volume to the > surface). > > See this thread: > > http://www.mail-archive.com/caret-users%40brainvis.wustl.edu/msg02081.html > > Also see the "Check Alignment between Normalized Volume and Surface" > section here: > > http://brainvis.wustl.edu/help/pals_volume_normalization/spm5_normalization_pals.html > > Examining the surface contour overlaid on the volum in volume view All is > often very enlightening. > > > On Aug 11, 2015, at 4:42 AM, j...@nbrc.ac.in wrote: > >>> >> yes, ours is an individual s surface reconstruction, and so we checked >> the >> registration in spm8( using anatomical image used for reconstruction >> and >> the functional image volumes used for mapping), where the volumes are >> coregistered properly, but shows anomaly in caret. >> >> thank you >> >> >> >> This almost always is because the functional volume is not >>> stereotactically registered to the anatomical volume used to generate >>> the >>> fiducial surface. Is this an atlas surface (e.g., one of the PALS mean >>> midthickness surfaces), or is it an individual's surface >>> reconstruction? >>> If atlas, this could happen if you were trying to map SPM functional >>> data >>> to the AFNI mid thickness surface, for example, because there are >>> noticeable differences between those stereotaxic spaces. >>> >>> If individual, make sure the functional volume is in register with the >>> anatomical volume used to generate the surface. >>> >>> >>> On Aug 10, 2015, at 1:40 AM, j...@nbrc.ac.in wrote: >>> >>>> Hi, >>>> when i map the functional data onto caret fiducial surface, it >>>> appears >>>> that the mapping is shifted in rostrocaudal axis, caudally, by about 2 >>>> -3 mm. anyone has idea what could be possibly wrong here? >>>> thanks, >>>> john >>>> _______________________________________________ >>>> caret-users mailing list >>>> caret-users@brainvis.wustl.edu >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
