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
