It might indeed help someone.  I was surprised to see it worked, until I saw 
what you did to make it work.  Clever.


On Nov 1, 2011, at 11:28 AM, Colin Reveley wrote:

> Caret will segment macaque (and presumably human, with a big computer) data 
> at 0.25mm, and the surface does reflect the anatomy (or the MRI) better than 
> downsampled to 0.5mm.
> 
> In doing this I was motivated by issues with freesurfer and the position of 
> the cerbellum and hindbrain in my ex-vivo data.
> 
> but since I had the volume I thought I'd see if caret/surefit works.
> 
> I removed the entire cerebellum, and everything from the top of the pons down 
> from the niftii.
> 
> This was semi manual - I made an initial mask by making fidicual surfaces of 
> each hemisphere in caret from 0.5mm downsampled, expanding them (not 
> inflating them) so that they look sort of pial and then doing surface -> 
> segmentation volume (to the entire 0.25mm original volume)
> 
> I used those, combined, as an ROI in the "mango" program. I tweaked that (1-6 
> hours, depending on level of perfectionism) and removed the CB and hindbrain.
> 
> then I made a caret surface in the usual way, all segmentation options on 
> except "remove hindbrain", from the 0.25 data without CB.
> 
> I used a Linux computer with 24GB of RAM. You need that.
> 
> Obviously it takes a long time to run, but it does look good.
> 
> it is handy for surface <-> volume, possibly also the extra accuracy might 
> help with registration. In my data for example the central sulcus is wide 
> with an ill defined fundus at 0.5mm dowsampled. at 0.25 the course of the 
> fundus is very clear and distinct.
> 
> hope this helps someone else too.
> 
> 
> 
> On 29 October 2011 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 97, Issue 4 (Donna Dierker)
> 
> 
> ---------- Forwarded message ----------
> From: Donna Dierker <[email protected]>
> To: "Caret, SureFit, and SuMS software users" <[email protected]>
> Date: Fri, 28 Oct 2011 12:46:01 -0500
> Subject: Re: [caret-users] caret-users Digest, Vol 97, Issue 4
> Also have a look at this:
> 
>      caret_command -spec-file-change-resolution
>         Change (typically reduce) the resolution of the surface
>         the list below, a close resolution is found by dividing
>                             will not be copied.  Any absolute or
>            data files in the spec file will be an ABSOLUTE path
>            since an absolute path is used to specify the spec file.
>            the data files in the spec file will be an absolute path
> 
> 
> On Oct 26, 2011, at 1:22 PM, Colin Reveley wrote:
> 
> > thanks donna - I'll try that.
> >
> > for the record, looking at it, I think:
> >
> > if the goal is to have a surface with the number of nodes you'd get from 
> > 0.25 data, in order to make volume <-> surface transfers (e.g. metric data) 
> > more accurate then:
> >
> > I think making the surface at 0.5, then upsampling the segmentation vol 
> > that results, then generating a hi-res surface from the anatomical volume 
> > and the upsampled segmentation (tweaked if one wants) is good enough.
> >
> > that is, I think the surface at 0.5 is good. so it's just about increasing 
> > node to voxel correspondence for the hi res volume.
> >
> > for that, I think maybe one does not need to segment at 0.25, although it 
> > might be nice, and more accurate.
> >
> > I have done this. I think It's "good enough".
> >
> > Colin
> >
> > On 26 October 2011 12:00, <[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 97, Issue 2 (Donna Dierker)
> >
> >
> > ---------- Forwarded message ----------
> > From: Donna Dierker <[email protected]>
> > To: "Caret, SureFit, and SuMS software users" 
> > <[email protected]>
> > Date: Tue, 25 Oct 2011 14:12:08 -0500
> > Subject: Re: [caret-users] caret-users Digest, Vol 97, Issue 2
> > I'd have to step through the source (which is available) to be sure, but I 
> > think not only do you need to check the hindbrain, but also it needs to 
> > find an object of decent size to disconnect -- something it thinks is the 
> > cerebellum, thresholded -- to be happy.  Else you'll get an error about 
> > disconnecting hindbrain failing.
> >
> > I can't quickly point to the Caret source; you'd have to download it and 
> > find it.  But here is an old SureFit script that covered the logic:
> >
> > http://surefit.cvs.sourceforge.net/viewvc/surefit/SureFitSrc/SureFitPython/Scripts.py?revision=1.13&view=markup
> >
> > Search for SegmentCerebralWhiteMatter and DISCONNECT HINDBRAIN SECTION.
> >
> >
> > On Oct 25, 2011, at 1:42 PM, Colin Reveley wrote:
> >
> > > ok -
> > >
> > > yes, it does seem as if freesurfer, then freesurfer to caret (there is a 
> > > recent VE tutorial on that, by which I mean a freesurfer to F99 tutorial, 
> > > although it doesn;t help with freesurfer itself. It does give nice 
> > > landmarks though.) is an option.
> > >
> > > Equally, it seems as though removing the hindbrain and cerebellum and 
> > > then running segmentation with those options unchecked might work.
> > >
> > > an upsampled version of the cerebral hull segmentation generated at 0.5mm 
> > > should facilitate that, and make it only work rather than loads  of work.
> > >
> > > but are there other issues than hindbrain, eye stuff, cut CC?
> > >
> > > is it worth trying to remove hindbrain manually?
> > >
> > >
> > >
> > > On 25 October 2011 10:03, <[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: hi res macaque (wolf zinke)
> > >   2. Re: hi res macaque (Donna Dierker)
> > >   3. Re: hi res macaque (Donna Dierker)
> > >
> > >
> > > ---------- Forwarded message ----------
> > > From: wolf zinke <[email protected]>
> > > To: "Caret, SureFit, and SuMS software users" 
> > > <[email protected]>
> > > Date: Tue, 25 Oct 2011 14:54:24 +0200
> > > Subject: Re: [caret-users] hi res macaque
> > > Hi,
> > >
> > > I had a similiar question a while ago, that was related to your issues. 
> > > At this time there was no 64 bit version of caret available, and hence I 
> > > ran into memory troubles with a high resolution monkey file (do you use 
> > > the 64 bit version of caret?).
> > >
> > > However, Donna Dierker gave me some pointers, why it would be problematic 
> > > to use a voxel size different from 0.5 mm. I am not sure, if this is 
> > > still true, but that might be a reason for your problem. I myself had 
> > > also the impression, that for the segmentation a resolution of 0.25 mm 
> > > would be very beneficial.
> > >
> > > I hope that this information helps,
> > > wolf
> > >
> > >> Hi,
> > >>
> > >> Thanks for the clarification. Currently,I am running caret on the 0.5 mm 
> > >> resolution and it overall gives good results, but fails in occipital 
> > >> regions. However, with your information I have a good reason to stick to 
> > >> the 0.5 mm resolution - makes the manual correction faster anyway.
> > >>
> > >> thanks for the reply,
> > >> wolf
> > >>
> > >>
> > >>
> > >> On 01/28/2010 04:03 PM, Donna Dierker wrote:
> > >> Setting aside the memory/64-bit question, there are assumptions built 
> > >> into the SureFit algorithm that assume voxdims for monkeys around 
> > >> 0.5-0.75mm cubed.  For example, there are routines in the hindbrain 
> > >> removal that are based on number of *slices* from the AC, and if you 
> > >> double the resolution, those will be off by a factor of two.  In short, 
> > >> it will fail.
> > >>
> > >> Try downsampling to 0.5 and making sure you crop to left and right hems. 
> > >>  If the problems persist, upload your anatomical volume here:
> > >>
> > >> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
> > >>
> > >> On 01/28/2010 07:30 AM, wolf zinke wrote:
> > >>> Hi,
> > >>>
> > >>> Sorry that I did not reply directly to this thread, but I did not find 
> > >>> any option for this reply.
> > >>>
> > >>> Is there a reason why caret is not build for 64 bit systems? I tried to 
> > >>> run a segmentation on macaque data with 0.25 mm voxel size, hoping to 
> > >>> get better results due to the resoltion. However, Caret threw an error 
> > >>> about insufficient memory, which first puzzled me since the PC got 
> > >>> 32GB. But than I realized that due to the 32 bit, Caret is not able to 
> > >>> address more than 4GB of the RAM, right?
> > >>>
> > >>> cheers,
> > >>> wolf
> > >
> > >
> > > On 25/10/11 08:30, Colin Reveley wrote:
> > >> I wonder if the bits of spine and the affine to to (deskulled, 
> > >> upsampled) F99 are an issue.
> > >>
> > >> I don't recall, but it's hugely likely I tried with rigid body too, i.e. 
> > >> without the bit cut off at bottom.
> > >>
> > >> On 25 October 2011 00:53, Colin Reveley <[email protected]> wrote:
> > >>
> > >> Hello.
> > >>
> > >> I have macaque data that is 0.25mm. I like that. I can do things with it 
> > >> that are more than cosmetic.
> > >>
> > >> The data was taken with a fancy brukker, and the contrast is very good 
> > >> from the sequence used. so good I wonder if it's a problem (it's a 
> > >> FLASH_MTR - it does correlate to T1 really closely, but contrast GM-WM 
> > >> is clearer. and there may be differences.)
> > >>
> > >> Thus far, I've been downsampling to 0.5 to make CARET surfaces.
> > >>
> > >> I'm beginning to suspect that, for my project, there is profit in a 
> > >> surface made at 0.25, with many nodes.
> > >>
> > >> what I am interested in is the really quite small region (in absolute 
> > >> terms) that was the subject of the paper by lewis and van essen in 2000.
> > >>
> > >> even though the F99 atlas does not have 300,000 nodes the paint, border 
> > >> and metric data are scalable and my own data would indeed support a 
> > >> hi-res surface, and benefit from it.
> > >>
> > >> I've got RAM.
> > >>
> > >> but I never managed to get far with 0.25.
> > >>
> > >> segmentation fails with hindbrain at any resolution below 0.5.
> > >>
> > >> I didn't mind. But now I think (I really do) I have a good reason to 
> > >> seek surface construction directly from my structural data at 0.25mm.
> > >>
> > >> So: is it possible? caret_command ... -res=X ?
> > >>
> > >> my data is ex-vivo. And probably no more than 1% of nonGM or nonWM 
> > >> voxels are nonzero. no ventricles. nothing. I did that. A mistake maybe.
> > >>
> > >> If I segment at 0.5, upsample to 0.25 and generate a surface with my 
> > >> data it works. CARET can make the surface.
> > >>
> > >> but segmentation does not work.
> > >>
> > >> appreciate help.
> > >>
> > >> Colin
> > >>
> > >>
> > >> _______________________________________________
> > >> 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]>
> > > Date: Tue, 25 Oct 2011 09:33:07 -0500
> > > Subject: Re: [caret-users] hi res macaque
> > > Sorry I don't have time to read this more carefully, but I'm swamped this 
> > > week.
> > >
> > > But the quick scan leads me to believe this is an issue with you trying 
> > > to segment monkey data at a resolution above 0.5mm.
> > >
> > > The problem is that some of the routines (e.g., especially 
> > > eye/skull/hindbrain removal) depend on the number of slices away from the 
> > > AC something is.  If the number of slices is twice what it expects, it 
> > > won't work.  You can turn off eye/skull removal, but as you already know, 
> > > de-checking hindbrain just makes it fail.
> > >
> > > Caret's segmentation has its limits, and this is now where our 
> > > development effort is focused these days.  Sorry.
> > >
> > > I know some people have gotten Freesurfer to segment monkey data, but I 
> > > suspect there are tricks/tweaks, and I do not know them.  I don't know 
> > > how the talairach.xfm stuff (and that which depends on it) works, for 
> > > example.  Obviously MNI305 won't work as a target.
> > >
> > >
> > > On Oct 25, 2011, at 7:54 AM, wolf zinke wrote:
> > >
> > > > Hi,
> > > >
> > > > I had a similiar question a while ago, that was related to your issues. 
> > > > At this time there was no 64 bit version of caret available, and hence 
> > > > I ran into memory troubles with a high resolution monkey file (do you 
> > > > use the 64 bit version of caret?).
> > > >
> > > > However, Donna Dierker gave me some pointers, why it would be 
> > > > problematic to use a voxel size different from 0.5 mm. I am not sure, 
> > > > if this is still true, but that might be a reason for your problem. I 
> > > > myself had also the impression, that for the segmentation a resolution 
> > > > of 0.25 mm would be very beneficial.
> > > >
> > > > I hope that this information helps,
> > > > wolf
> > > >
> > > >> Hi,
> > > >>
> > > >> Thanks for the clarification. Currently,I am running caret on the 0.5 
> > > >> mm resolution and it overall gives good results, but fails in 
> > > >> occipital regions. However, with your information I have a good reason 
> > > >> to stick to the 0.5 mm resolution - makes the manual correction faster 
> > > >> anyway.
> > > >>
> > > >> thanks for the reply,
> > > >> wolf
> > > >>
> > > >>
> > > >>
> > > >> On 01/28/2010 04:03 PM, Donna Dierker wrote:
> > > >> Setting aside the memory/64-bit question, there are assumptions built 
> > > >> into the SureFit algorithm that assume voxdims for monkeys around 
> > > >> 0.5-0.75mm cubed.  For example, there are routines in the hindbrain 
> > > >> removal that are based on number of *slices* from the AC, and if you 
> > > >> double the resolution, those will be off by a factor of two.  In 
> > > >> short, it will fail.
> > > >>
> > > >> Try downsampling to 0.5 and making sure you crop to left and right 
> > > >> hems.  If the problems persist, upload your anatomical volume here:
> > > >>
> > > >> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
> > > >>
> > > >> On 01/28/2010 07:30 AM, wolf zinke wrote:
> > > >>> Hi,
> > > >>>
> > > >>> Sorry that I did not reply directly to this thread, but I did not 
> > > >>> find any option for this reply.
> > > >>>
> > > >>> Is there a reason why caret is not build for 64 bit systems? I tried 
> > > >>> to run a segmentation on macaque data with 0.25 mm voxel size, hoping 
> > > >>> to get better results due to the resoltion. However, Caret threw an 
> > > >>> error about insufficient memory, which first puzzled me since the PC 
> > > >>> got 32GB. But than I realized that due to the 32 bit, Caret is not 
> > > >>> able to address more than 4GB of the RAM, right?
> > > >>>
> > > >>> cheers,
> > > >>> wolf
> > > >
> > > >
> > > > On 25/10/11 08:30, Colin Reveley wrote:
> > > >> I wonder if the bits of spine and the affine to to (deskulled, 
> > > >> upsampled) F99 are an issue.
> > > >>
> > > >> I don't recall, but it's hugely likely I tried with rigid body too, 
> > > >> i.e. without the bit cut off at bottom.
> > > >>
> > > >> On 25 October 2011 00:53, Colin Reveley <[email protected]> wrote:
> > > >>
> > > >> Hello.
> > > >>
> > > >> I have macaque data that is 0.25mm. I like that. I can do things with 
> > > >> it that are more than cosmetic.
> > > >>
> > > >> The data was taken with a fancy brukker, and the contrast is very good 
> > > >> from the sequence used. so good I wonder if it's a problem (it's a 
> > > >> FLASH_MTR - it does correlate to T1 really closely, but contrast GM-WM 
> > > >> is clearer. and there may be differences.)
> > > >>
> > > >> Thus far, I've been downsampling to 0.5 to make CARET surfaces.
> > > >>
> > > >> I'm beginning to suspect that, for my project, there is profit in a 
> > > >> surface made at 0.25, with many nodes.
> > > >>
> > > >> what I am interested in is the really quite small region (in absolute 
> > > >> terms) that was the subject of the paper by lewis and van essen in 
> > > >> 2000.
> > > >>
> > > >> even though the F99 atlas does not have 300,000 nodes the paint, 
> > > >> border and metric data are scalable and my own data would indeed 
> > > >> support a hi-res surface, and benefit from it.
> > > >>
> > > >> I've got RAM.
> > > >>
> > > >> but I never managed to get far with 0.25.
> > > >>
> > > >> segmentation fails with hindbrain at any resolution below 0.5.
> > > >>
> > > >> I didn't mind. But now I think (I really do) I have a good reason to 
> > > >> seek surface construction directly from my structural data at 0.25mm.
> > > >>
> > > >> So: is it possible? caret_command ... -res=X ?
> > > >>
> > > >> my data is ex-vivo. And probably no more than 1% of nonGM or nonWM 
> > > >> voxels are nonzero. no ventricles. nothing. I did that. A mistake 
> > > >> maybe.
> > > >>
> > > >> If I segment at 0.5, upsample to 0.25 and generate a surface with my 
> > > >> data it works. CARET can make the surface.
> > > >>
> > > >> but segmentation does not work.
> > > >>
> > > >> appreciate help.
> > > >>
> > > >> 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
> > >
> > >
> > >
> > >
> > >
> > > ---------- Forwarded message ----------
> > > From: Donna Dierker <[email protected]>
> > > To: "Caret, SureFit, and SuMS software users" 
> > > <[email protected]>
> > > Date: Tue, 25 Oct 2011 10:00:35 -0500
> > > Subject: Re: [caret-users] hi res macaque
> > > "this is now where our development effort is focused these days" should 
> > > have read "this is NOT where our development effort is focused these days"
> > >
> > > On Oct 25, 2011, at 9:33 AM, Donna Dierker wrote:
> > >
> > > > Sorry I don't have time to read this more carefully, but I'm swamped 
> > > > this week.
> > > >
> > > > But the quick scan leads me to believe this is an issue with you trying 
> > > > to segment monkey data at a resolution above 0.5mm.
> > > >
> > > > The problem is that some of the routines (e.g., especially 
> > > > eye/skull/hindbrain removal) depend on the number of slices away from 
> > > > the AC something is.  If the number of slices is twice what it expects, 
> > > > it won't work.  You can turn off eye/skull removal, but as you already 
> > > > know, de-checking hindbrain just makes it fail.
> > > >
> > > > Caret's segmentation has its limits, and this is now where our 
> > > > development effort is focused these days.  Sorry.
> > > >
> > > > I know some people have gotten Freesurfer to segment monkey data, but I 
> > > > suspect there are tricks/tweaks, and I do not know them.  I don't know 
> > > > how the talairach.xfm stuff (and that which depends on it) works, for 
> > > > example.  Obviously MNI305 won't work as a target.
> > > >
> > > >
> > > > On Oct 25, 2011, at 7:54 AM, wolf zinke wrote:
> > > >
> > > >> Hi,
> > > >>
> > > >> I had a similiar question a while ago, that was related to your 
> > > >> issues. At this time there was no 64 bit version of caret available, 
> > > >> and hence I ran into memory troubles with a high resolution monkey 
> > > >> file (do you use the 64 bit version of caret?).
> > > >>
> > > >> However, Donna Dierker gave me some pointers, why it would be 
> > > >> problematic to use a voxel size different from 0.5 mm. I am not sure, 
> > > >> if this is still true, but that might be a reason for your problem. I 
> > > >> myself had also the impression, that for the segmentation a resolution 
> > > >> of 0.25 mm would be very beneficial.
> > > >>
> > > >> I hope that this information helps,
> > > >> wolf
> > > >>
> > > >>> Hi,
> > > >>>
> > > >>> Thanks for the clarification. Currently,I am running caret on the 0.5 
> > > >>> mm resolution and it overall gives good results, but fails in 
> > > >>> occipital regions. However, with your information I have a good 
> > > >>> reason to stick to the 0.5 mm resolution - makes the manual 
> > > >>> correction faster anyway.
> > > >>>
> > > >>> thanks for the reply,
> > > >>> wolf
> > > >>>
> > > >>>
> > > >>>
> > > >>> On 01/28/2010 04:03 PM, Donna Dierker wrote:
> > > >>> Setting aside the memory/64-bit question, there are assumptions built 
> > > >>> into the SureFit algorithm that assume voxdims for monkeys around 
> > > >>> 0.5-0.75mm cubed.  For example, there are routines in the hindbrain 
> > > >>> removal that are based on number of *slices* from the AC, and if you 
> > > >>> double the resolution, those will be off by a factor of two.  In 
> > > >>> short, it will fail.
> > > >>>
> > > >>> Try downsampling to 0.5 and making sure you crop to left and right 
> > > >>> hems.  If the problems persist, upload your anatomical volume here:
> > > >>>
> > > >>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
> > > >>>
> > > >>> On 01/28/2010 07:30 AM, wolf zinke wrote:
> > > >>>> Hi,
> > > >>>>
> > > >>>> Sorry that I did not reply directly to this thread, but I did not 
> > > >>>> find any option for this reply.
> > > >>>>
> > > >>>> Is there a reason why caret is not build for 64 bit systems? I tried 
> > > >>>> to run a segmentation on macaque data with 0.25 mm voxel size, 
> > > >>>> hoping to get better results due to the resoltion. However, Caret 
> > > >>>> threw an error about insufficient memory, which first puzzled me 
> > > >>>> since the PC got 32GB. But than I realized that due to the 32 bit, 
> > > >>>> Caret is not able to address more than 4GB of the RAM, right?
> > > >>>>
> > > >>>> cheers,
> > > >>>> wolf
> > > >>
> > > >>
> > > >> On 25/10/11 08:30, Colin Reveley wrote:
> > > >>> I wonder if the bits of spine and the affine to to (deskulled, 
> > > >>> upsampled) F99 are an issue.
> > > >>>
> > > >>> I don't recall, but it's hugely likely I tried with rigid body too, 
> > > >>> i.e. without the bit cut off at bottom.
> > > >>>
> > > >>> On 25 October 2011 00:53, Colin Reveley <[email protected]> wrote:
> > > >>>
> > > >>> Hello.
> > > >>>
> > > >>> I have macaque data that is 0.25mm. I like that. I can do things with 
> > > >>> it that are more than cosmetic.
> > > >>>
> > > >>> The data was taken with a fancy brukker, and the contrast is very 
> > > >>> good from the sequence used. so good I wonder if it's a problem (it's 
> > > >>> a FLASH_MTR - it does correlate to T1 really closely, but contrast 
> > > >>> GM-WM is clearer. and there may be differences.)
> > > >>>
> > > >>> Thus far, I've been downsampling to 0.5 to make CARET surfaces.
> > > >>>
> > > >>> I'm beginning to suspect that, for my project, there is profit in a 
> > > >>> surface made at 0.25, with many nodes.
> > > >>>
> > > >>> what I am interested in is the really quite small region (in absolute 
> > > >>> terms) that was the subject of the paper by lewis and van essen in 
> > > >>> 2000.
> > > >>>
> > > >>> even though the F99 atlas does not have 300,000 nodes the paint, 
> > > >>> border and metric data are scalable and my own data would indeed 
> > > >>> support a hi-res surface, and benefit from it.
> > > >>>
> > > >>> I've got RAM.
> > > >>>
> > > >>> but I never managed to get far with 0.25.
> > > >>>
> > > >>> segmentation fails with hindbrain at any resolution below 0.5.
> > > >>>
> > > >>> I didn't mind. But now I think (I really do) I have a good reason to 
> > > >>> seek surface construction directly from my structural data at 0.25mm.
> > > >>>
> > > >>> So: is it possible? caret_command ... -res=X ?
> > > >>>
> > > >>> my data is ex-vivo. And probably no more than 1% of nonGM or nonWM 
> > > >>> voxels are nonzero. no ventricles. nothing. I did that. A mistake 
> > > >>> maybe.
> > > >>>
> > > >>> If I segment at 0.5, upsample to 0.25 and generate a surface with my 
> > > >>> data it works. CARET can make the surface.
> > > >>>
> > > >>> but segmentation does not work.
> > > >>>
> > > >>> appreciate help.
> > > >>>
> > > >>> 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
> > > >
> > > >
> > > > _______________________________________________
> > > > 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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