thanks matt. I talked it out with doug at freesurfer, and the fake t1 strategy is definitely best. in fact I'll use it for monkey too.
the level of work depends on how high resolution, and how accurate you want to be. but the surfaces are great, require no topology alteration or smoothing, and you can put one at the boundary, or just in the wm, or just in the gm as you please. it's great, the work is worth it. unless you have 2000 subjects. On 28 August 2012 19:17, <[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 107, Issue 8 (Matt Glasser) > > > ---------- Forwarded message ---------- > From: Matt Glasser <[email protected]> > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Cc: > Date: Tue, 28 Aug 2012 13:12:55 -0500 > Subject: Re: [caret-users] caret-users Digest, Vol 107, Issue 8 > 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 <[email protected]> > Reply-To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Date: Tuesday, August 28, 2012 12:16 PM > To: <[email protected]> > 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, <[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: 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 <[email protected]> >> To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> 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, <[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: Inner white matter (Donna Dierker) >> > >> > >> > ---------- Forwarded message ---------- >> > From: Donna Dierker <[email protected]> >> > To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> > 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 >> > > [email protected] >> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > >> > >> > >> > >> > _______________________________________________ >> > caret-users mailing list >> > [email protected] >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > >> > >> > >> <d1_f1_occip.png><f1_occip_3class.png>_______________________________________________ >> > caret-users mailing list >> > [email protected] >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> >> >> >> ---------- Forwarded message ---------- >> From: Colin Reveley <[email protected]> >> To: "[email protected]" <[email protected]> >> 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 >>> [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..." >>> >> >> >> ---------- Forwarded message ---------- >> From: Timothy Coalson <[email protected]> >> To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> 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 >> <[email protected]> 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, <[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: Inner white matter (Donna Dierker) >> >> >> >> >> >> ---------- Forwarded message ---------- >> >> From: Donna Dierker <[email protected]> >> >> To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> >> 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 >> >> > [email protected] >> >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> caret-users mailing list >> >> [email protected] >> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> >> >> >> >> <d1_f1_occip.png><f1_occip_3class.png>_______________________________________________ >> >> 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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