Thanks Donna & David for your suggestions! I actually used FLIRT instead of FNIRT to normalize my data.
I tried the Conte69 atlas (again using the FLIRT space during surface mapping) and still couldn't see the precuneus cluster. I'll try Donna's suggestions to see what's going on. -- Dale > Today's Topics: > > 1. A precuneus cluster disappeared after surface projection > (Ping-Hui Chiu) > 2. Re: A precuneus cluster disappeared after surface projection > (Donna Dierker) > 3. Re: A precuneus cluster disappeared after surface projection > (David Van Essen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 15 Sep 2012 11:18:11 -0600 > From: Ping-Hui Chiu <chiuping...@gmail.com> > Subject: [caret-users] A precuneus cluster disappeared after surface > projection > To: caret-users@brainvis.wustl.edu > Message-ID: > < > canbyug5d3epceq7gqk+1hs22h9y+xov1negyrpqmtw1531j...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://brainvis.wustl.edu/pipermail/caret-users/attachments/20120915/2fda699e/attachment-0001.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: precuneus.nii.gz > Type: application/x-gzip > Size: 3769 bytes > Desc: not available > Url : > http://brainvis.wustl.edu/pipermail/caret-users/attachments/20120915/2fda699e/attachment-0001.gz > > ------------------------------ > > Message: 2 > Date: Sat, 15 Sep 2012 19:18:20 -0500 > From: Donna Dierker <donna.dier...@sbcglobal.net> > Subject: Re: [caret-users] A precuneus cluster disappeared after > surface projection > To: "Caret, SureFit, and SuMS software users" > <caret-users@brainvis.wustl.edu> > Message-ID: <d438bec6-6f57-4d4f-8e85-af698cb41...@sbcglobal.net> > Content-Type: text/plain; charset=iso-8859-1 > > 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 > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > ------------------------------ > > Message: 3 > Date: Sat, 15 Sep 2012 22:34:28 -0500 > From: David Van Essen <vanes...@wustl.edu> > Subject: Re: [caret-users] A precuneus cluster disappeared after > surface projection > To: "Caret, SureFit, and SuMS software users" > <caret-users@brainvis.wustl.edu> > Message-ID: <cb079117-e2d7-4000-ace0-00686b220...@wustl.edu> > Content-Type: text/plain; charset=us-ascii > > 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 > >> caret-users@brainvis.wustl.edu > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > ------------------------------ > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > End of caret-users Digest, Vol 108, Issue 4 > ******************************************* >
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