I would add to Colin's advice to toggle on D/C Volume contours (bottom of page selection list). Make sure the surface selection in the contours menu matches the surface used for projecting paint to volume. Make sure the surface aligns well with the volume. (Sometimes these spec files can have multiple versions of surfaces/volumes, some pairings of which align better than others.)
This will alert you to any issues with a mismatch between the stereotaxic spaces of surface and volume. On Nov 18, 2013, at 9:43 PM, Colin Reveley <[email protected]> wrote: > In step 4 (or somewhere) don't set the space to F99 necessarily but do say > "get parameters from a volume file" and choose the F99 T1 shown in your > images. possibly make the strip a bit thinner so it doesn't overlap. > > presumably it all looks aligned in "surface and volume" view? I think "get > parameters from volume file" will take care of it, but it's memory based > information. > > best, > > Colin R > > > On 19 November 2013 03:00, <[email protected]> wrote: > Send caret-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://brainvis.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > Today's Topics: > > 1. F99 surface-to-volume mapping (David Grayson) > > > ---------- Forwarded message ---------- > From: David Grayson <[email protected]> > To: <[email protected]> > Cc: > Date: Mon, 18 Nov 2013 18:57:49 -0800 > Subject: [caret-users] F99 surface-to-volume mapping > Dear Caret Users, > > I have been using the F99 atlas and the accompanying parcellations available > with the "Macaque.F99.BOTH-HEMS.STANDARD-SCENES.73730.spec" package. I have a > question about the surface-to-volume mapping with this atlas. > > It appears that when I map one of these parcellations to volume space, the > resulting volume is not mapped accurately onto the true cortical ribbon. I > have provided examples in the attached .png files. The most blatant issue is > in the OFC and frontal polar regions, which are too caudal, but this is true > for much of the occipital lobe as well. From the sagittal and coronal views, > it's also clear that much of the parcellation is too dorsal. These > discrepancies are also there in what's already available in volume space > within the downloadable package, in the parcellation file > 'Macaque.F99UA1.BOTH.LewisVE00.nii.gz'. > > Are there perhaps any important fixes that have been made, or perhaps > additional steps beyond the basic 'convert paint column to paint volume' tool > that should be taken to perform a more accurate mapping from surface to > volume? Here are precisely the steps that I took: > > 1) load Macaque.F99.BOTH-HEMS.STANDARD-SCENES.73730.spec, select right hem > fiducial, composite areacolor, and composite paint > 2) display Paxinos parcellation on right hem fiducial > 3) Attributes--> paint --> convert paint column to paint volume > 4) leave all default settings, except change "space" to 'MACAQUE-F99'. click > OK. > 5) Save new volume using File --> Save Data File > > Any insights will be much appreciated. Thank you very much, > > David > > _______________________________________________ > 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
