I think it's Volume: Segmentation: Fill Cavities. You can't just leave it at fill cavities, because projecting from surface to each of the pial and white surfaces will result in voxels outside the ribbon, even if you do optimize thickness for each. You need to mask the result using the ribbon. (David sent you an alternate way of computing the ribbon, but Matt said that route's ribbon was not more accurate than Freesurfer's, which presumably you already have, if you have white and pial surfaces.)
Mask is a better verb than subtract. You still have a problem with how you combine the white and pial projections; you can use the "Max" function using Caret's volume math ops or fslmaths. But you consider working with one paint/label at a time, in case one region projects to the white, but an adjacent region projects to the pial. The higher paint index wins, and this is probably not what you want. If you can script this in such a way that processing one region at a time is not onerous, then you will have yourself a not-easy way of doing this. On Jan 3, 2012, at 12:55 PM, Colin Reveley wrote: > the freesurfer ribbon volume is just a GM segmentation right? > > why not leave at just "fill cavaties" (I didn't know that existed, that seems > the key thing)? > > On 3 January 2012 18:00, <[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. Re: painting the entire GM thickness accurately from surface > data (Donna Dierker) > 2. Fwd: error in overlay (Donna Dierker) > > > ---------- Forwarded message ---------- > From: Donna Dierker <[email protected]> > To: "Caret, SureFit, and SuMS software users" <[email protected]> > Cc: > Date: Tue, 3 Jan 2012 09:43:46 -0600 > Subject: Re: [caret-users] painting the entire GM thickness accurately from > surface data > I just don't think there is an easy way to do this in Caret right now, but I > know that won't stop you. ;-) > > You might try something like this: > > map surf paint to vol using white, specifying outer thickness >0 > map surf paint to vol using pial, specifying inner thickness >0 > union these volumes and fill cavities > subtract the result from the Freesurfer ribbon volume > min the resulting difference at 0 > > > On Dec 31, 2011, at 11:43 AM, Colin Reveley wrote: > > > Hi - (happy new year) > > > > Caret has a nice feature that lets you drop paints from a surface into a > > volume. > > > > but one thing is that all it really allows is for one to specifiy a > > distance above and below the suface. So, it does not allow one to fill the > > gray matter of a volume with paint accurately. > > > > But, I can fill the gray or white matter accurately by having a pial or > > white surface (from freesurfer), turning them into segmentations and > > subtracting one from the other. > > > > Or, wisely avoiding freesurfer, I could make a segmentation of the entire > > volume (threshold to segmentation), shrink a midthickness surface made with > > surefit so it pretty much fits the WM and subtract a segmentation of that > > from the volume segmentation. > > > > So, is there a way, could there be a way, might there one day be a way of > > moving paint data from surface to volume using a segmentation (derived from > > wherever) as a template, so that the entire cortical thickness is labelled > > by the paint volume, and accounting for thickness variation? > > > > this would be pretty handy. I could see it helping lots of things (for > > example the scabalebrainatlas). > > > > since I have a mask/segmentation of gray matter maybe there's a trick that > > I could use to accomplish this right now? > > > > All I can think of is to use the white, mid and pial surfaces I have (and > > maybe 2 more surfaces, the average of white and mid and of pial and mid), > > make paint volumes and OR them all togther. > > > > best for 2012. > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ---------- Forwarded message ---------- > From: Donna Dierker <[email protected]> > To: and SuMS software users Caret SureFit <[email protected]> > Cc: > Date: Tue, 3 Jan 2012 09:55:35 -0600 > Subject: [caret-users] Fwd: error in overlay > This ended up off-line, but was resolved by switching to an English character > set. > > > Begin forwarded message: > > > From: Donna Dierker <[email protected]> > > Date: December 30, 2011 1:58:51 PM CST > > To: [email protected] > > Subject: Re: [caret-users] error in overlay > > > > You can map cubic 2mm functional volumes. It should be no problem, > > provided the orientation and origin are accurately specified in the NIFTI > > header. If the volume is not NIFTI format, there can be issues. > > > > However, neither of these explains the specific error you are getting, > > which concerns the metric output file. By any chance are you using a > > non-English character set on your computer? I've never come across this > > particular error before, but it has been a problem in other I/O contexts. > > If this is a potential issue, then how much of a hassle would it be to try > > Caret on another computer with an English character set? > > > > > > On Dec 30, 2011, at 1:33 PM, vin . wrote: > > > >> thanx Donna, > >> > >> just checked, have write permission > >> Just, I tried again with metric name > >> ''map_data_0_30_Dec_2011_20_29_06.metric'' > >> > >> still same message. > >> > >> http://prefrontal.org/blog/2009/04/using-caret-for-fmri-visualization/ > >> do u think, the above mentioned procedure is fine, if I use MNI space 2mm > >> group results for overlaying ? or I need to transform them, before > >> overlapping them in to PALS_fmri_mapping_atlasfile (as described in the > >> above link ) > >> > >> Thank you > >> > >> On Fri, Dec 30, 2011 at 6:51 PM, Donna Dierker <[email protected]> > >> wrote: > >> Hmmm. That's odd. What filename did you use? Any spaces or characters > >> other than alphanumeric? Did it perhaps include a path that doesn't > >> exist? Finally, do you have write permission to the current directory, or > >> valid specified path? > >> > >> > >> On Dec 30, 2011, at 10:50 AM, vin . wrote: > >> > >>> Thank you Donna, > >>> > >>> It was specified. even I tried changing name of it. still same error. > >>> > >>> > >>> On Thu, Dec 29, 2011 at 6:45 PM, Donna Dierker <[email protected]> > >>> wrote: > >>> Make sure your metric filename is not empty; see attached capture for > >>> where it is specified. > >>> > >>> > >>> > >>> > >>> On Dec 29, 2011, at 10:22 AM, vin . wrote: > >>> > >>>> Dear Caret Experts, > >>>> > >>>> A newbie to Caret, having problem to overlay .. getting error '' > >>>> A metric file must be provided for metric mapping '' > >>>> > >>>> I followed this tutorial. Would like to overlay, few surface tracking > >>>> results in Caret surface (Atlas) > >>>> http://prefrontal.org/blog/2009/04/using-caret-for-fmri-visualization/ > >>>> > >>>> Thank you :) > >>>> _______________________________________________ > >>>> 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 > > > _______________________________________________ > 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
