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
