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
