Re: [caret-users] A precuneus cluster disappeared after surface projection

2012-09-17 Thread Ping-Hui Chiu
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
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 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

2012-09-17 Thread Matt Glasser
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 --
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 --
 
 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