Maybe I'm missing something, but would mapping to volume from the midthickness surface, with a thickness value greater than the maximum cortical thickness value, and then masking with the ribbon volume give you what you want?
Tim On Wed, Jan 4, 2012 at 9:13 AM, Donna Dierker <[email protected]>wrote: > 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 >
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