Could you upload your dataset in a zip archive here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Specifically I need: * functional volume being mapped * anatomical volume with which functional volume aligns * anatomical volume used to generate segmentation -- *cropped* * fiducial coord file * topology file I am wondering if the centers of the volumes between the cropped volume used to generate the surface and the whole brain anatomical volume. On Aug 12, 2015, at 1:11 AM, j...@nbrc.ac.in wrote: >> > > 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 _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
