Hi Colin, thanks a lot! Best Pablo
2013/7/8 Colin Reveley <[email protected]> > What you should do is: > > extract F99 from the skull. extract the MNI atlas from the skull. > > alternatively, you might get good results by putting both the MNI and > F99 image into ACPC and cropping them so that the non-brain material is > nearly the same. but you might not. > > it's best to brain extract them. I can give you this if you need it. I'm > not sure where by extracted MNI is but I do have one. > > applying SUSAN noise reduction to F99 is a good idea. > > you can then apply registration software to F99. And you can apply > transforms to caret paint volumes that you've made by using caret's > function to make paint volumes from paint columns. It is not perfect to the > actual cortical thickness of course but you can play with the parameters. > > I doubt linear registration is going to do the trick. > > You might find that using fnirt is quite hard and slow. > > You might ask the mni people. > > You might try this. This will work. This is ours actually. you will need > an NVIDIA GPU that is less than 3 years old and is meant for science or > intensive computer games. > > http://www.bss.phy.cam.ac.uk/~ag492/ezys/ > > I never did manage to get the mni labelling to be of actual use. maybe > that has changed. > > but you can put paint data from caret into mni like this. > > good luck. Let me know if I can help. I've done a lot of this. > > you can generate the equvalent of the attached images. > > actually it would be interesting to compare the paxinos labels on MNI > made this way, and made the way they did it. > > with perseverance you can do more less anything you need. Our software > does help, if you have the appropriate hardware. > > you could also try to make a surface from the MNI data (so downsample to > 0.5mm). you will need to pre-process it a lot with FAST or nu_correct or > both. it might not work. > > then you can try surface registration methods. > > best, > > Colin > > > On 8 July 2013 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. F99 to MNI (Pablo Barttfeld) >> 2. Re: F99 to MNI (Donna Dierker) >> 3. Re: F99 to MNI (Matt Glasser) >> 4. Re: F99 to MNI (Pablo Barttfeld) >> 5. Re: F99 to MNI (Donna Dierker) >> >> >> ---------- Forwarded message ---------- >> From: Pablo Barttfeld <[email protected]> >> To: <[email protected]> >> Cc: >> Date: Mon, 8 Jul 2013 11:37:35 +0200 >> Subject: [caret-users] F99 to MNI >> Hi all, >> I would like to map the regions in F99 into MNI space, is there a >> function in Caret to do that? >> Best >> Pablo >> >> >> >> >> ---------- Forwarded message ---------- >> From: Donna Dierker <[email protected]> >> To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> Cc: >> Date: Mon, 8 Jul 2013 08:54:25 -0500 >> Subject: Re: [caret-users] F99 to MNI >> I'm pretty sure you're the first person to ask that question. Or at >> least the first I've heard it. >> >> Obviously the macaque and human brains have different scales, but it >> might, in principle, be possible. Computing a volumetric transform from >> the F99 individual monkey volume to either MNI305 or avg152T1 mean human >> atlases doesn't seem likely to work well. >> >> But I think David registered the F99 surface to the same 73730 mesh as >> the PALS human atlas. (He had a good reason for doing so.) If that is in >> the Sept 2006 tutorial dataset, then you could load the F99 paint areas on >> the PALS atlas and use Attributes: Paint to project them from surface-land >> to volume-land, using the PALS flirt, SPM, or MRITOTAL surface as the >> mapping substrate. >> >> Hopefully David will chime in if the F99-to-PALS correspondence makes >> this a bad idea. >> >> (Let's face it: We must always approach cross-species registration with >> a long list of caveats.) >> >> >> On Jul 8, 2013, at 4:37 AM, Pablo Barttfeld <[email protected]> >> wrote: >> >> > Hi all, >> > I would like to map the regions in F99 into MNI space, is there a >> function in Caret to do that? >> > Best >> > Pablo >> > >> > >> > _______________________________________________ >> > caret-users mailing list >> > [email protected] >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> >> >> >> ---------- Forwarded message ---------- >> From: Matt Glasser <[email protected]> >> To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> Cc: >> Date: Mon, 8 Jul 2013 09:53:44 -0500 >> Subject: Re: [caret-users] F99 to MNI >> I cannot imagine being able to do this well with volumetric registration. >> >> Matt. >> >> On 7/8/13 8:54 AM, "Donna Dierker" <[email protected]> wrote: >> >> >I'm pretty sure you're the first person to ask that question. Or at >> >least the first I've heard it. >> > >> >Obviously the macaque and human brains have different scales, but it >> >might, in principle, be possible. Computing a volumetric transform from >> >the F99 individual monkey volume to either MNI305 or avg152T1 mean human >> >atlases doesn't seem likely to work well. >> > >> >But I think David registered the F99 surface to the same 73730 mesh as >> >the PALS human atlas. (He had a good reason for doing so.) If that is >> >in the Sept 2006 tutorial dataset, then you could load the F99 paint >> >areas on the PALS atlas and use Attributes: Paint to project them from >> >surface-land to volume-land, using the PALS flirt, SPM, or MRITOTAL >> >surface as the mapping substrate. >> > >> >Hopefully David will chime in if the F99-to-PALS correspondence makes >> >this a bad idea. >> > >> >(Let's face it: We must always approach cross-species registration with >> >a long list of caveats.) >> > >> > >> >On Jul 8, 2013, at 4:37 AM, Pablo Barttfeld <[email protected]> >> >wrote: >> > >> >> Hi all, >> >> I would like to map the regions in F99 into MNI space, is there a >> >>function in Caret to do that? >> >> Best >> >> Pablo >> >> >> >> >> >> _______________________________________________ >> >> 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 >> >> >> >> >> >> ---------- Forwarded message ---------- >> From: Pablo Barttfeld <[email protected]> >> To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> Cc: >> Date: Mon, 8 Jul 2013 16:01:55 +0200 >> Subject: Re: [caret-users] F99 to MNI >> Hi Donna, thanks for your response. >> Sorry I was not clear enough, I meant the macaque MNI space, not the >> human MNI. >> thanks a lot >> Pablo >> >> >> 2013/7/8 Donna Dierker <[email protected]> >> >>> I'm pretty sure you're the first person to ask that question. Or at >>> least the first I've heard it. >>> >>> Obviously the macaque and human brains have different scales, but it >>> might, in principle, be possible. Computing a volumetric transform from >>> the F99 individual monkey volume to either MNI305 or avg152T1 mean human >>> atlases doesn't seem likely to work well. >>> >>> But I think David registered the F99 surface to the same 73730 mesh as >>> the PALS human atlas. (He had a good reason for doing so.) If that is in >>> the Sept 2006 tutorial dataset, then you could load the F99 paint areas on >>> the PALS atlas and use Attributes: Paint to project them from surface-land >>> to volume-land, using the PALS flirt, SPM, or MRITOTAL surface as the >>> mapping substrate. >>> >>> Hopefully David will chime in if the F99-to-PALS correspondence makes >>> this a bad idea. >>> >>> (Let's face it: We must always approach cross-species registration with >>> a long list of caveats.) >>> >>> >>> On Jul 8, 2013, at 4:37 AM, Pablo Barttfeld <[email protected]> >>> wrote: >>> >>> > Hi all, >>> > I would like to map the regions in F99 into MNI space, is there a >>> function in Caret to do that? >>> > Best >>> > Pablo >>> > >>> > >>> > _______________________________________________ >>> > 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 >>> >> >> >> >> ---------- Forwarded message ---------- >> From: Donna Dierker <[email protected]> >> To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> Cc: >> Date: Mon, 8 Jul 2013 10:28:52 -0500 >> Subject: Re: [caret-users] F99 to MNI >> Hi Pablo, >> >> Sorry -- this is the first I have heard of it. Pretty cool: >> >> http://www.bic.mni.mcgill.ca/ServicesAtlases/Macaque >> >> If someone has registered the F99 atlas to this one, I am unaware of it >> (just as I was unaware of the MNI macaque atlas until you educated me). >> >> Donald McLaren registered his 112RM atlas to F99; that's here: >> >> MCLAREN_EtAl_2009 >> http://sumsdb.wustl.edu/sums/directory.do?id=6716882 >> >> Donna >> >> >> On Jul 8, 2013, at 9:01 AM, Pablo Barttfeld <[email protected]> >> wrote: >> >> > Hi Donna, thanks for your response. >> > Sorry I was not clear enough, I meant the macaque MNI space, not the >> human MNI. >> > thanks a lot >> > Pablo >> > >> > >> > 2013/7/8 Donna Dierker <[email protected]> >> > I'm pretty sure you're the first person to ask that question. Or at >> least the first I've heard it. >> > >> > Obviously the macaque and human brains have different scales, but it >> might, in principle, be possible. Computing a volumetric transform from >> the F99 individual monkey volume to either MNI305 or avg152T1 mean human >> atlases doesn't seem likely to work well. >> > >> > But I think David registered the F99 surface to the same 73730 mesh as >> the PALS human atlas. (He had a good reason for doing so.) If that is in >> the Sept 2006 tutorial dataset, then you could load the F99 paint areas on >> the PALS atlas and use Attributes: Paint to project them from surface-land >> to volume-land, using the PALS flirt, SPM, or MRITOTAL surface as the >> mapping substrate. >> > >> > Hopefully David will chime in if the F99-to-PALS correspondence makes >> this a bad idea. >> > >> > (Let's face it: We must always approach cross-species registration >> with a long list of caveats.) >> > >> > >> > On Jul 8, 2013, at 4:37 AM, Pablo Barttfeld <[email protected]> >> wrote: >> > >> > > Hi all, >> > > I would like to map the regions in F99 into MNI space, is there a >> function in Caret to do that? >> > > Best >> > > Pablo >> > > >> > > >> > > _______________________________________________ >> > > 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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