Re: [caret-users] A precuneus cluster disappeared after surface projection
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
Re: [caret-users] A precuneus cluster disappeared after surface projection
You would probably have the most success with a fully surface-based pipeline (i.e. project the minimally preprocessed time series on the individual subject's surfaces and analyze and average them there). This is something we are working on together with the FSL group to make available in the future. Peace, Matt. From: Ping-Hui Chiu chiuping...@gmail.com Reply-To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Date: Monday, September 17, 2012 11:33 AM To: caret-users@brainvis.wustl.edu Subject: Re: [caret-users] A precuneus cluster disappeared after surface projection 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 mailto:canbyug5d3epceq7gqk%2b1hs22h9y%2bxov1negyrpqmtw1531j...@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
Re: [caret-users] A precuneus cluster disappeared after surface projection
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=8291494dir_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
