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 > >
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