> you'd go above and also below into the wm as well, if I follow you. That > seems certainly one way to try, although the thing might be that paint > regions intersect in places doing it like that. > > thanks very much for comments I never computed the ribbon actually in FS. > and anything to avoid more FS. I'm sure it's great for human but it's > pretty hands on and tricky with macaque. It took ages. doubtless a ribbon > volume is just a one line command at this stage though. > >
> On 5 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: caret-users Digest, Vol 100, Issue 2 (Timothy Coalson) >> >> >> ---------- Forwarded message ---------- >> From: Timothy Coalson <[email protected]> >> To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> Cc: >> Date: Wed, 4 Jan 2012 14:28:27 -0600 >> Subject: Re: [caret-users] caret-users Digest, Vol 100, Issue 2 >> 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 >>> >> >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >
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