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 > >
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