that's great, re: whole headthanks. Very pleased about that. Half would not have been a problem (I could cut mine in half. Donna. Then they'd both be in half :) indeed mirror it.) Both halves even better. thanks.
I used bet myself, and cleaned manually. Quite some time ago. I presumed you folks did something like that when you made the surface, but maybe surefit works on a whole head scan. I've never tried it. So possibly the head extracted version I made is worth uploading, since I'm enormously perfectionist as you know. I'll have to check and be sure it's perfect though ;) thanks again Colin On 2 October 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: f99 volumes (Donna Dierker) > 2. Re: f99 volumes (Jochen Ditterich) > > > ---------- Forwarded message ---------- > From: Donna Dierker <[email protected]> > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Cc: > Date: Mon, 1 Oct 2012 11:09:32 -0500 > Subject: Re: [caret-users] f99 volumes > David might have more squirreled away on his machine somewhere, but I > couldn't find this in sumsdb or my archives. > > I'm sure some labs around here -- very likely the Snyder Lab -- have used > FSL's Brain Extraction Tool (BET) on the F99 atlas for various purposes, > but I'm not aware that they released anything like that for public > consumption. I do know from experience that the fractional intensity > threshold and gradient matter. Possibly loop through several permutations > and judge which combo you like best. > > There is a fullHead minc volume here: > > http://brainmap.wustl.edu/pub/donna/SAM/F99UA1.tar.gz > login pub > password download > > Bit it's 256x256x180 -- not 240. I don't think it's the most upstream > volume we have, but it's the most upstream one I could find. > > > On Sep 29, 2012, at 1:35 AM, Colin Reveley <[email protected]> wrote: > > > Two enquiries, one more important than the other. Less important first: > > > > 1) Is there a brain extracted version of the F99 scan anywhere (a > reference version)? > > > > I did do it myself, in fact took quite some time over it as I remember, > but maybe there is a reference version that's better. > > > > I want to use it for some non-linear registration research. you need to > register things that are definitely equivalent. And extracting monkey > perfectly isn't that easy. > > > > 2) More important thing: > > > > One thing I'll be doing is registering F99 to a T1 of the animal in the > attached image. That animal was, I'm told, in the same place at the same > time as F99. > > > > For that, I wonder if there is a copy of the entire F99 scan? > > > > That would have huge value to me. > > > > I may be quite wrong, but it's very possible the original scan was > 256x256x240 voxels and looked a lot like the attached picture. There's no > doubt F99 was acquired in a similar scanner because he's sitting up. I > don't think there are that many scanners like that. And I basically reckon > it was the same coil and same or similar sequence, but I could be totally > off. > > > > F99 is a really good scan in terms of artefact, in addition to being an > atlas reference (as is this animal, but a different kind of atlas), so if > you did have the entire thing that would be really great. We're in the > atlas business for a bit. Sort of. F99 would be a really nice scan to have, > for a bunch of reasons. It's unlikely we'd ever want to do more than > experiment with it but obviously we'd ask if we did anything worth knowing > about. > > > > I guess even if the scan was like that originally it's now long gone, > but if not....that would be lovely. > > > > many thanks, > > > > Colin R > > > > > > > > > > <wemeetagain.png>_______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ---------- Forwarded message ---------- > From: Jochen Ditterich <[email protected]> > To: <[email protected]> > Cc: > Date: Mon, 1 Oct 2012 10:42:56 -0700 > Subject: Re: [caret-users] f99 volumes > The F99 full head volume is also part of these two datasets in SumsDB: > > http://sumsdb.wustl.edu/sums/**archivelist.do?archive_id=** > 684661&archive_name=MACAQUE.**LEFT_HEM.04-01-29.tar.gz<http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=684661&archive_name=MACAQUE.LEFT_HEM.04-01-29.tar.gz> > > http://sumsdb.wustl.edu/sums/**archivelist.do?archive_id=** > 684673&archive_name=MACAQUE.**RIGHT_HEM.04-01-29.tar.gz<http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=684673&archive_name=MACAQUE.RIGHT_HEM.04-01-29.tar.gz> > > Cheers, > > Jochen > > On 10/1/2012 9:09 AM, Donna Dierker wrote: > >> David might have more squirreled away on his machine somewhere, but I >> couldn't find this in sumsdb or my archives. >> >> I'm sure some labs around here -- very likely the Snyder Lab -- have >> used FSL's Brain Extraction Tool (BET) on the F99 atlas for various >> purposes, but I'm not aware that they released anything like that for >> public consumption. I do know from experience that the fractional >> intensity threshold and gradient matter. Possibly loop through >> several permutations and judge which combo you like best. >> >> There is a fullHead minc volume here: >> >> http://brainmap.wustl.edu/pub/**donna/SAM/F99UA1.tar.gz<http://brainmap.wustl.edu/pub/donna/SAM/F99UA1.tar.gz>login >> pub >> password download >> >> Bit it's 256x256x180 -- not 240. I don't think it's the most >> upstream volume we have, but it's the most upstream one I could >> find. >> >> >> On Sep 29, 2012, at 1:35 AM, Colin Reveley <[email protected]> >> wrote: >> >> Two enquiries, one more important than the other. Less important >>> first: >>> >>> 1) Is there a brain extracted version of the F99 scan anywhere (a >>> reference version)? >>> >>> I did do it myself, in fact took quite some time over it as I >>> remember, but maybe there is a reference version that's better. >>> >>> I want to use it for some non-linear registration research. you >>> need to register things that are definitely equivalent. And >>> extracting monkey perfectly isn't that easy. >>> >>> 2) More important thing: >>> >>> One thing I'll be doing is registering F99 to a T1 of the animal in >>> the attached image. That animal was, I'm told, in the same place at >>> the same time as F99. >>> >>> For that, I wonder if there is a copy of the entire F99 scan? >>> >>> That would have huge value to me. >>> >>> I may be quite wrong, but it's very possible the original scan was >>> 256x256x240 voxels and looked a lot like the attached picture. >>> There's no doubt F99 was acquired in a similar scanner because he's >>> sitting up. I don't think there are that many scanners like that. >>> And I basically reckon it was the same coil and same or similar >>> sequence, but I could be totally off. >>> >>> F99 is a really good scan in terms of artefact, in addition to >>> being an atlas reference (as is this animal, but a different kind >>> of atlas), so if you did have the entire thing that would be really >>> great. We're in the atlas business for a bit. Sort of. F99 would be >>> a really nice scan to have, for a bunch of reasons. It's unlikely >>> we'd ever want to do more than experiment with it but obviously >>> we'd ask if we did anything worth knowing about. >>> >>> I guess even if the scan was like that originally it's now long >>> gone, but if not....that would be lovely. >>> >>> many thanks, >>> >>> Colin R >>> >>> >>> >>> >>> <wemeetagain.png>_____________**______________________________**____ >>> caret-users mailing list [email protected] >>> http://brainvis.wustl.edu/**mailman/listinfo/caret-users<http://brainvis.wustl.edu/mailman/listinfo/caret-users> >>> >> >> >> ______________________________**_________________ caret-users mailing >> list [email protected] >> http://brainvis.wustl.edu/**mailman/listinfo/caret-users<http://brainvis.wustl.edu/mailman/listinfo/caret-users> >> >> > -- > > ------------------------- > > Jochen Ditterich, Ph.D. > Associate Professor > Center for Neuroscience > University of California > 1544 Newton Court > Davis, CA 95618 > USA > > office: +1 (530) 754-5084 > lab: +1 (530) 754-6987 > fax: +1 (530) 757-8827 > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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