In addition, depending on your needs you may find some of the services at scalablebrainatlas.incf.org to be useful
there are volume projections of paxinos and others from caret onto F99 but with a subtler representation of the cortical thickness than caret's mapping permits. you can download the slices into matlab and reconstruct them into a nifti with the nifti toolbox. you'd have to set the dimensions and origin etc. you can generate a caret paint volume by converting to washu format with caret command and altering the header + generating an areacolor file for it from their table. another, simpler, option would be to import the volume and table you make, plus the caret spec into "connectome workbench". depending on your requirements. FSL or AFNI or whatever doable. Very good site as I say. Has lots of stuff. there's the viewer and at the top of the page "services" right hemisphere of F99. I think bisecting and mirroring everything to the left would be legitimate. could be wrong. Colin > 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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