YSL, The values get diluted, because they are being averaged across 12 subjects: The voxel intersects in some individuals, misses in others.
But if you enter a threshold (e.g., 3.47) in the mapping wizard, it will map the volume to each of the 12 subjects, thresholding at that value and calculating the suprathreshold area. Then it will calculate the mean suprathreshold area across all subjects and compute a secondary threshold for which the suprathreshold area is equal to the mean suprathreshold area. (The tutorial probably does a better job of explaining this than I just did.) The AFM mapping has the advantage that the t-stats (f-stats, whatever) don't get messed with; however, it has the downside of not always intersecting your blobs. There are other mapping algorithms besides enclosing voxel and interpolated voxel (e.g., MCW Brainfish or Gaussian) that might be worth trying for your purposes: http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MapVolumeToSurface#Mapping_Algorithm_Page Donna On 04/29/2010 05:27 AM, Yune S. Lee wrote: > Thanks for the help, Donna. > I've remapped onto the MFM. While mapping and intersecting seem to > better, for some reason, voxels don't appear at the same threshold > (t:3.47) that was applied to SPM rendering. > Enclosed is the screen captured figure and you can see that the color > on the foci is barely above 0. > I wonder if the t values in the SPM T map file get decreased when > mapping to MFM. > > Best, > YSL > > > On Wed, Apr 28, 2010 at 4:04 PM, Donna Dierker > <[email protected] <mailto:[email protected]>> wrote: > > YSL, > > I recommend reading through all of Caret_Tutorial_Sep22.pdf > (http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379), > section 1.22.2, starting on page 24, but this excerpt is worth > including here: "In AFM, each node is assigned the value of the > voxel in which it resides (or an interpolated value, depending on > the specific algorithm chosen). In MFM, each node takes the > average value after mapping the volume to each of the 12 > contributing hemispheres. MFM gives a smoother map and the best > estimate of spatial localization; AFM gives the most likely peak > value." > > Attached are several captures that illustrate what is going on: > > vol_intersect.jpg shows your functional volume overlaid on the > avg152T1.mnc structural volume with the SPM5 average fiducial > surface contour. The volume is a bit splotchy and sometimes the > clusters are just along the margins of the surface, rather than > centered over the surface contour. > inflated_lateral.jpg shows the lateral view of the AFM mapping to SPM5 > inflated_lateral_MFM.jpg shows the same view, but with MFM mapping > inflated_stg_sylvian.jpg shows what mapped to the medial bank of > the STG; SPM's view can't really show this, because it's buried > inflated_stg_sylvian_MFM.jpg shows the same view, but with MFM mapping > > So the upshot is that it does map/intersect -- just not always > optimally with AFM. MFM might be the better choice for your data. > > Hope this helps, > > Donna > > > On 04/28/2010 02:02 PM, Yune S. Lee wrote: > > Hi Donna, > I just uploaded the spm T map file. We ensured that left is > left and right is right for the analyze format. > Yes, I've chosen "show Mapping to Average Fiducial Surface" , > not the second one "Show Average of Mapping to All > multi-fiducial cases" > I didn't really know what the main differences are. Could you > explain the usage of each? > > Best, > YSL > > > > On Wed, Apr 28, 2010 at 2:28 PM, Donna Dierker > <[email protected] <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>> wrote: > > Probably the easiest way to get to the bottom of it is for > us to > look at > your functional volume. Could you upload it here: > > http://pulvinar.wustl.edu/cgi-bin/upload.cgi > > It appears that your cluster did not intersect the SPM5 average > fiducial > surface very well. I suspect you used AFM, rather than > MFM. The > latter > likely would have improved the intersection. > > On 04/28/2010 12:29 PM, Yune S. Lee wrote: > > > > Dear Caret users, > > > > I'm a bit puzzled by different activation foci between caret > and SPM5. > > I mapped the same T-map onto the > PALS_B12_standard_scenes.73730 > spec > > file for which I set SPM5 for mapping Atlas space. > > Nonetheless, the output results in the caret looks quite > different > > such that the STS activation that is clearly seen in the SPM > figure is > > missing in the caret. > > (See attached for the side-by-side comparison). I > wonder if I did > > something wrong during the volume mapping and any help > would be > greatly > > appreciated. > > > > Thanks, > > YSL > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > [email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > ------------------------------------------------------------------------ > > _______________________________________________ > caret-users mailing list > [email protected] > <mailto:[email protected]> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > _______________________________________________ > 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
