Mohamed et al., I am catching up on old emails and hence responding belatedly to this thread.
While we encourage investigators to use fully surface-based analysis and visualization methods as recommended by Matt, we are also mindful that there are various situations in which this may not currently be feasible. In such cases, a useful alternative can be to use foci files that represent the 3D location of the center of an ROI that can be projected to an atlas surface. The projection process preserves information about the distance between the focus and the nearest surface tile, thereby revealing whether it ‘missed by a mm or a mile’. This has been used extensively in Caret software and to date more selectively in wb_view. David On Aug 24, 2014, at 11:42 PM, Timothy Coalson <[email protected]> wrote: > It should also be noted that some of the mapping methods make point estimates > in the volume - specifically, trilinear, enclosing, and cubic - a surface has > no thickness to it, which could cause it to still miss some volume data, even > when using the individual's surfaces. Ribbon mapping will instead use all > voxels between the two surfaces specified (typically white and pial), so it > will not miss voxels in the same way. > > Tim > > > > On Sun, Aug 24, 2014 at 11:11 PM, Glasser, Matthew <[email protected]> > wrote: > We don’t recommend mapping volume smoothed/averaged data onto group average > surfaces. The correct way to do a surface-based analysis is to map the data > from each individual on to that individual’s surface and then register across > individuals on the surface (ideally using cortical areal features). Ideally > you will also have minimized smoothing. At this point you can average across > subjects. > > The reason the group average surface doesn’t appear to match the group > average volume is because individual subjects often have topologically > incompatible folding patterns (in some regions of cortex), which, when > averaged across subjects tends to shrink the surfaces in those areas (and the > pial surfaces more than the white surfaces). > > Peace, > > Matt. > > From: Mohamed Tawfik <[email protected]> > Date: Sunday, August 24, 2014 at 8:28 PM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] Inquiry regarding volume to surface mapping > > Hi all, > > I am using Connectome workbench to visualize my searchlight analysis and > statistical significance results on an inflated brain. I use volume to > surface mapping to convert my .nii files to surface files for visualization. > While being successful in most cases, yet, in some cases where the > significant voxels are are close on the boundary between the grey and white > matter, these clusters totally disappear on the surface images (while they > are visible on volumes). As demonstrated in the attached figure, The surface > outline is more lateral to the significant cluster , thus, making it appear > in the volume images but not on the surface images. > > Is there a way to be able to demonstrate these cluster on the surface images > of the inflated brain ? > > Any help will be appreciated. > > Respectfully yours, > > Mohamed. > > <vol_surf.png> > > <vol_surf2.png> > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
