Hello Dale, If Donna's explanation is correct (as I suspect is the case), you may have better results using the Conte69 atlas surface that is registered to the FNIRT MNI152 volume, In general, we are encouraging investigators to migrate to this atlas for a number of reasons, including the fact that this will be the atlas surface used by the Human Connectome Project. To learn more about the Conte69 atlas surfaces, visit http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas.
To download the atlas datasets, go to http://sumsdb.wustl.edu/sums/directory.do?id=8291494&dir_name=CONTE69 and decide on which datasets are useful for you - they differ in the mesh (74k or 164k) and data format (caret5 and Connectome Workbench). The Readme includes information about how to migrate data from the PALS-B12 74k mesh to the Conte69 164k mesh. I hope this helps. If questions or problems arise, please let us know. David VE On Sep 15, 2012, at 7:18 PM, Donna Dierker wrote: > Dale, > > In situations like this, I get the anatomical template image used as the > atlas target for spatial normalization. Flirt and fnirt both use the > avg152T1, but different versions. Load your atlas target in Caret, and > overlay the surface outline of the PALS mean surface used as a mapping > substrate. Then load your precuneus cluster volume and overlay that over > all. You might need help at one or more of these steps, but this is how you > will get to the bottom of the missing cluster. > > If you used fnirt to get stuff on avg152, then there's a decent chance your > cluster won't intersect the mean PALS surface well. Seeing the intersection > of the anatomical volume, mean surface, and functional volume will tell us > how to fix the problem. > > Donna > > > On Sep 15, 2012, at 12:18 PM, Ping-Hui Chiu wrote: > >> Dear Caret experts, >> >> I've been using Caret v5.65 without any problems but today I found that the >> attached contrast can't be seen on the PALS_B12 surface. >> >> This contrast shows a precuneus cluster of intensity 0.999 (33 voxels >> surrounding 4/-72/46 in the MNI152 space). It can be seen just fine by >> FSLView & Mango in the volume space. However, it disappeared after surface >> projection using the FLIRT space and various mapping algorithms, such as >> METRIC_ENCLOSING_VOXEL, METRIC_MAXIMUM_VOXEL with neighbor box size=0, etc. >> >> It doesn't look like a threshold problem because I still can't see it with a >> 0 threshold. What may be wrong here? Any hints will surely be helpful! >> >> Thanks! >> Dale >> <precuneus.nii.gz>_______________________________________________ >> 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
