Yes, it would indeed rely on being able to mask out the overflow. The reason I thought that such intersection wouldn't be an issue is that I would hope that the mapping method takes appropriate measures to resolve such conflicts, probably by using the label from the closest surface node. This seems like it would be a better conflict resolution than "max" or "first wins", which is basically what you are left using if you try to map it in multiple from-surface steps. You should be able to generate appropriate masking volumes with caret5's surface to segmentation volume option, so you shouldn't need the FS ribbon specifically.
Unfortunately, I hear that freesurfer's command to generate ribbon volume is slower than it should be, but it is just barely possible that it would only need the 4 surfaces (left/right pial/white) to give the ribbon (note that the ribbon volume is a label volume, labels 3 and 42 give the right and left gray matter, if i recall). Tim On Thu, Jan 5, 2012 at 12:22 PM, Colin Reveley <[email protected]> wrote: > > 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 >>> >>> >> > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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