There is no tessellation algorithm in workbench, and it is unlikely there will one any time soon. This is because we are using FreeSurfer to generate surfaces now and focusing our development on new things related to brain connectivity. If you sent me one of your images I could see if I can think of any way to make it more palatable for FreeSurfer...
Peace, Matt. From: Colin Reveley <cm...@sussex.ac.uk> Reply-To: "Caret, SureFit, and SuMS software users" <caret-users@brainvis.wustl.edu> Date: Tuesday, August 28, 2012 12:16 PM To: <caret-users@brainvis.wustl.edu> Subject: Re: [caret-users] caret-users Digest, Vol 107, Issue 8 Tim - thanks that's really helpful. I now have two options: your suggestion (faster) or simply making a fake T1 for freesurfer, which will work perfectly but is most certainly very time consuming and very boring. I have the workbench public beta. Presumably that's enough? thanks again, really helpful. I appreciate it. tell me, can I use the workbench public beta to generate pial and wm surfaces? Freesurfer cannot do this because the caudal gray matter has higher intensity than rostral white matter. marmosets don't have much up front there. the way around is to create a fake, idealised "T1" based on the real data. it isn't fun. and there are quite a few scans here to do. but as I say, surefit made a very sensible midthickness indeed. It would sure save me time, energy and pain if I could generate at least "good enough to play around with" pial and white surfaces without having to make an artificial T1 for freesurfer. thanks again. Colin On 28 August 2012 18:00, <caret-users-requ...@brainvis.wustl.edu> wrote: > Send caret-users mailing list submissions to > caret-users@brainvis.wustl.edu > > 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 > caret-users-requ...@brainvis.wustl.edu > > You can reach the person managing the list at > caret-users-ow...@brainvis.wustl.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > Today's Topics: > > 1. Re: inner white matter (Donna Dierker) > 2. Re: caret-users Digest, Vol 107, Issue 7 (Colin Reveley) > 3. Re: inner white matter (Timothy Coalson) > > > ---------- Forwarded message ---------- > From: Donna Dierker <do...@brainvis.wustl.edu> > To: "Caret, SureFit, and SuMS software users" <caret-users@brainvis.wustl.edu> > Cc: > Date: Mon, 27 Aug 2012 10:04:05 -0500 > Subject: Re: [caret-users] inner white matter > Pretty pictures, but I still don't get why you want to scale down the surface, > then scale it back up. > > I could see lying to a volume header, or resampling the anatomical, to get > SureFit to behave better. And if you do that, you would need to rescale the > surface to get rid of the deliberately mis-stated resolution in the volume > header. > > > On Aug 26, 2012, at 6:43 PM, Colin Reveley wrote: > >> > >> > I don't think it makes sense at in human, or rhesus. >> > >> > however in marmoset the caudal white matter (which is really most of the >> white matter) is arranged in a sort of nested shell type deal. the inner >> white matter is the most myelinated, mainly its seems mostly the optic >> radation. but not only that. >> > >> > the principle diffusoion direction of the outer shell seems orthogonal to >> the inner. and there is a very clear boundary. >> > >> > so one might want to map DTI maps, FA and etc etc between these shells to >> characterise the WM. >> > >> > here are a couple of picture at 100um showing what I mean. >> > >> > it can only possibly work when the anatomy is like this, and also no >> folding >> > >> > probably not even then >> > >> > but if it did work I can map ev's, vol ratio, myelin, lattice index, loads >> of measures. and hence learn more about marmoset anatomy. >> > >> > which is a new thing for me. there's nearly nothing on its WM structure in >> the literature. I'm trying to figure it out. >> > >> > It's an idea. no more. >> > >> > On 25 August 2012 18:00, <caret-users-requ...@brainvis.wustl.edu> wrote: >> > Send caret-users mailing list submissions to >> > caret-users@brainvis.wustl.edu >> > >> > 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 >> > caret-users-requ...@brainvis.wustl.edu >> > >> > You can reach the person managing the list at >> > caret-users-ow...@brainvis.wustl.edu >> > >> > When replying, please edit your Subject line so it is more specific >> > than "Re: Contents of caret-users digest..." >> > >> > Today's Topics: >> > >> > 1. Re: Inner white matter (Donna Dierker) >> > >> > >> > ---------- Forwarded message ---------- >> > From: Donna Dierker <do...@brainvis.wustl.edu> >> > To: "Caret, SureFit, and SuMS software users" >> <caret-users@brainvis.wustl.edu> >> > Cc: >> > Date: Fri, 24 Aug 2012 13:17:17 -0500 >> > Subject: Re: [caret-users] Inner white matter >> > Go here: >> > >> > http://www.nitrc.org/frs/download.php/2871/GIFTI_Surface_Format.pdf >> > >> > On page 36, it says: The application of a CoordinateSystemTransformMatrix, >> places the coordinates into the system shown in the table below. All >> coordinates are in millimeters. >> > >> > So sorry: You don't get to change units. >> > >> > But I know I'm not the only one scratching my head wondering why you want >> to do this. Oh, I know the occasional temptation to lie in a volume header, >> to elicit certain software behavior. >> > >> > But I've never been tempted to do it on a surface. I've scaled surfaces >> for real (e.g., if I had to lie in a header when segmenting a smaller mammal, >> to get SureFit to do the right thing). But not to get surfaces to behave >> properly. So I guess I'm curious. >> > >> > Because what you describe below seems to me to be the equivalent of taking >> x,y,z axes; lining out the indices and writing numbers 1/4 the size of the >> original marks; and then lining those through and writing the original marks >> down. Which means I'm almost certainly not getting what you asked. >> > >> > >> > On Aug 24, 2012, at 1:47 AM, Colin Reveley wrote: >> > >>> > > Would it be possible to shrink a surface with a scaling matrix, and then >>> define the mesh as being in the same space as the original. >>> > > >>> > > E.g a mesh at 1mm scaled down to eg 0.25mm and then redefined as a 1mm >>> surface? >>> > > >>> > > The notion here is to generate an outer and inner pair of white matter >>> surfaces. Of course there are issues. >>> > > >>> > > The general notion is to then treat these as white and pial surfaces, >>> take their mean and map white matter data using matt's method for mapping >>> gray matter data (scalar diffusion maps). >>> > > >>> > > This is less nuts than it sounds in marmoset because the white matter is >>> simple topologically and in terms of gross anatomy , particularly in the >>> caudal half of the brain. >>> > > >>> > > In principle there should be a mid thickness line in much of the brains >>> white matter. >>> > > >>> > > With a nifti you just change the units in the header. I don't appear to >>> see a gifti equivalent. >>> > > >>> > > Thanks >>> > > >>> > > Colin >>> > > _______________________________________________ >>> > > caret-users mailing list >>> > > caret-users@brainvis.wustl.edu >>> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > >> > >> > >> > >> > _______________________________________________ >> > caret-users mailing list >> > caret-users@brainvis.wustl.edu >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > >> > >> > >> <d1_f1_occip.png><f1_occip_3class.png>_______________________________________ >> ________ >> > caret-users mailing list >> > caret-users@brainvis.wustl.edu >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ---------- Forwarded message ---------- > From: Colin Reveley <cm...@sussex.ac.uk> > To: "caret-users@brainvis.wustl.edu" <caret-users@brainvis.wustl.edu> > Cc: > Date: Mon, 27 Aug 2012 17:07:12 +0100 > Subject: Re: [caret-users] caret-users Digest, Vol 107, Issue 7 > So to be just totally clear: what I actually want is this: > > If you look at the figures I attached you'll see two main components: the gm > and wm, characterised by signal intensity. We can use that to make a line at > the wm/gm and another at pial and we obtain two surfaces enclosing the gm. > > But in my figures, in this animal, note that there is a both a clear boundary > and clear intensity change within the white matter. Just like wm/gm. > > So I want to make a surface that treats this inner boundary as if it were a > gm/wm boundary. In order to characterise the properties of wm in those > regions. > > Thinking about it, the best move may be to cut out the gm, and treat the outer > shell as if it's gm. Freesurfer might then compute what I want . That's better > than linear contraction. But harder. Yet More staring at 3 million > voxels...but that's ok. > > Unless there's a surfeit trick/hack or something....surfeit made a marmoset > mid thickness that was plausible. That's impressive. With freesurfer I have to > make a fake volume by hand. > > Marmosets are the only primate that is germ line transgenic. So you can make a > colony of marmosets with parkinsonism in principle. It has a small brain so > you can scan at high res. It is small and easy to house compared to rhesus. It > has twins twice a year. It's adult in 2 years. > > It's the model animal of the future...ask the folks in Japan :). > > Thanks > > Colin. > > On Monday, 27 August 2012, wrote: >> Send caret-users mailing list submissions to >> caret-users@brainvis.wustl.edu >> >> 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 >> caret-users-requ...@brainvis.wustl.edu >> >> You can reach the person managing the list at >> caret-users-ow...@brainvis.wustl.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of caret-users digest..." > > > ---------- Forwarded message ---------- > From: Timothy Coalson <tsc...@mst.edu> > To: "Caret, SureFit, and SuMS software users" <caret-users@brainvis.wustl.edu> > Cc: > Date: Mon, 27 Aug 2012 13:26:47 -0500 > Subject: Re: [caret-users] inner white matter > Okay, taking a shot in the dark here, but if what you want is the WM > surface, except thinner between sides, rescaling the surface is > unlikely to give you what you want, since it will also bring > everything towards some point in the volume, so with that hook shape > in the image, the inside edge will move into GM while the outside > moves into the WM, and even if that picture is deceptive as to the 3D > structure, it will cut off a larger portion of WM on a gyrus than in a > sulcus. > > However, I have a possibility you can try. Get workbench installed if > you haven't yet, and try "wb_command -create-signed-distance-volume" > with the WM surface (after converting it to .surf.gii). Note that its > default distance is sized for a human brain, so you will probably want > to use the -exact-limit and -approx-limit options. Then, threshold > the new volume into a segmentation at a negative number equal to how > many mm you want to trim from the WM, and generate a surface from it > in caret5. It may not be a particularly smooth surface, but it should > end up about where you want it, in theory (if you have something that > can take a real-valued volume and generate a surface at a particular > level set, it may give you a smoother surface, but I don't know of > such a utility). > > Tim > > On Mon, Aug 27, 2012 at 10:04 AM, Donna Dierker > <do...@brainvis.wustl.edu> wrote: >> > Pretty pictures, but I still don't get why you want to scale down the >> surface, then scale it back up. >> > >> > I could see lying to a volume header, or resampling the anatomical, to get >> SureFit to behave better. And if you do that, you would need to rescale the >> surface to get rid of the deliberately mis-stated resolution in the volume >> header. >> > >> > >> > On Aug 26, 2012, at 6:43 PM, Colin Reveley wrote: >> > >>> >> >>> >> I don't think it makes sense at in human, or rhesus. >>> >> >>> >> however in marmoset the caudal white matter (which is really most of the >>> white matter) is arranged in a sort of nested shell type deal. the inner >>> white matter is the most myelinated, mainly its seems mostly the optic >>> radation. but not only that. >>> >> >>> >> the principle diffusoion direction of the outer shell seems orthogonal to >>> the inner. and there is a very clear boundary. >>> >> >>> >> so one might want to map DTI maps, FA and etc etc between these shells to >>> characterise the WM. >>> >> >>> >> here are a couple of picture at 100um showing what I mean. >>> >> >>> >> it can only possibly work when the anatomy is like this, and also no >>> folding >>> >> >>> >> probably not even then >>> >> >>> >> but if it did work I can map ev's, vol ratio, myelin, lattice index, >>> loads of measures. and hence learn more about marmoset anatomy. >>> >> >>> >> which is a new thing for me. there's nearly nothing on its WM structure >>> in the literature. I'm trying to figure it out. >>> >> >>> >> It's an idea. no more. >>> >> >>> >> On 25 August 2012 18:00, <caret-users-requ...@brainvis.wustl.edu> wrote: >>> >> Send caret-users mailing list submissions to >>> >> caret-users@brainvis.wustl.edu >>> >> >>> >> 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 >>> >> caret-users-requ...@brainvis.wustl.edu >>> >> >>> >> You can reach the person managing the list at >>> >> caret-users-ow...@brainvis.wustl.edu >>> >> >>> >> When replying, please edit your Subject line so it is more specific >>> >> than "Re: Contents of caret-users digest..." >>> >> >>> >> Today's Topics: >>> >> >>> >> 1. Re: Inner white matter (Donna Dierker) >>> >> >>> >> >>> >> ---------- Forwarded message ---------- >>> >> From: Donna Dierker <do...@brainvis.wustl.edu> >>> >> To: "Caret, SureFit, and SuMS software users" >>> <caret-users@brainvis.wustl.edu> >>> >> Cc: >>> >> Date: Fri, 24 Aug 2012 13:17:17 -0500 >>> >> Subject: Re: [caret-users] Inner white matter >>> >> Go here: >>> >> >>> >> http://www.nitrc.org/frs/download.php/2871/GIFTI_Surface_Format.pdf >>> >> >>> >> On page 36, it says: The application of a >>> CoordinateSystemTransformMatrix, places the coordinates into the system >>> shown in the table below. All coordinates are in millimeters. >>> >> >>> >> So sorry: You don't get to change units. >>> >> >>> >> But I know I'm not the only one scratching my head wondering why you want >>> to do this. Oh, I know the occasional temptation to lie in a volume header, >>> to elicit certain software behavior. >>> >> >>> >> But I've never been tempted to do it on a surface. I've scaled surfaces >>> for real (e.g., if I had to lie in a header when segmenting a smaller >>> mammal, to get SureFit to do the right thing). But not to get surfaces to >>> behave properly. So I guess I'm curious. >>> >> >>> >> Because what you describe below seems to me to be the equivalent of >>> taking x,y,z axes; lining out the indices and writing numbers 1/4 the size >>> of the original marks; and then lining those through and writing the >>> original marks down. Which means I'm almost certainly not getting what you >>> asked. >>> >> >>> >> >>> >> On Aug 24, 2012, at 1:47 AM, Colin Reveley wrote: >>> >> >>>> >> > Would it be possible to shrink a surface with a scaling matrix, and >>>> then define the mesh as being in the same space as the original. >>>> >> > >>>> >> > E.g a mesh at 1mm scaled down to eg 0.25mm and then redefined as a 1mm >>>> surface? >>>> >> > >>>> >> > The notion here is to generate an outer and inner pair of white matter >>>> surfaces. Of course there are issues. >>>> >> > >>>> >> > The general notion is to then treat these as white and pial surfaces, >>>> take their mean and map white matter data using matt's method for mapping >>>> gray matter data (scalar diffusion maps). >>>> >> > >>>> >> > This is less nuts than it sounds in marmoset because the white matter >>>> is simple topologically and in terms of gross anatomy , particularly in the >>>> caudal half of the brain. >>>> >> > >>>> >> > In principle there should be a mid thickness line in much of the >>>> brains white matter. >>>> >> > >>>> >> > With a nifti you just change the units in the header. I don't appear >>>> to see a gifti equivalent. >>>> >> > >>>> >> > Thanks >>>> >> > >>>> >> > Colin >>>> >> > _______________________________________________ >>>> >> > caret-users mailing list >>>> >> > caret-users@brainvis.wustl.edu >>>> >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >> >>> >> >>> >> >>> >> >>> >> _______________________________________________ >>> >> caret-users mailing list >>> >> caret-users@brainvis.wustl.edu >>> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >> >>> >> >>> >> >>> <d1_f1_occip.png><f1_occip_3class.png>______________________________________ >>> _________ >>> >> caret-users mailing list >>> >> caret-users@brainvis.wustl.edu >>> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > >> > >> > _______________________________________________ >> > caret-users mailing list >> > caret-users@brainvis.wustl.edu >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
_______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
