[caret-users] RE: Communicating with AFNI (Rishi)

Rishi Kalwani rmkalwani at hotmail.com
Mon Mar 17 09:31:02 CDT 2008


Hi David, 

I almost always use the Volume-Surface Visualization Tools within Caret 
to view the linkages between my volume and surface.  

However, I have a functional volume that is being represented differently in 
Caret and AFNI.  The voxel values have a different range within Caret and AFNI.  
Somehow, the voxels take on a different range of intensities (i.e. 1-25) in AFNI than 
in Caret (i.e. 1-8).  I'm not sure what's happening here.  But the data within 
AFNI is more consistent with the original data.  

Anyway, these voxels represent sites at which electrophysiological data was obtained.  
We're trying to quantify the overlap between these sites and atlas cortical areas.   Thus, the 
registered surface is very useful here.  
 
Nonetheless, I'm having trouble with the correspondence between the AFNI volume and the Caret Surface. 
I have created a transformation matrix file that has all the appropriate info (Volume Name, Coordinate File Name, AC coords, Volume Dimensions). 
here it is: 

BeginHeader
date 22 Jan 2002 14:40:44
comment 
encoding ASCII
EndHeader
tag-transformation-matrix-file-version 2
tag-number-of-matrices 1
tag-end-of-tags
tag-matrix-name Map to 711-2B.111 Talairach
tag-matrix-comment +88,122,73 to 711-2B_AS.111
tag-matrix-target-volume-name series003.LEFT_HEM+orig.nii+tlrc.HEAD
tag-matrix-target-volume-dimensions 65 156 102
tag-matrix-fiducial-coord-name Macaque.Cyrus.L.Fiducial.2007-08-17.26377.coord
tag-matrix-target-AC-coords 64 60 44
tag-matrix-begin
1.000000 0.000000 0.000000 64.000000 
0.000000 1.000000 0.000000 60.000000 
0.000000 0.000000 1.000000 44.000000 
0.000000 0.000000 0.000000 1.000000 

I think the critical parameter is the AC coords.  I have used several different values for this (obtained from viewing the volume origin
in Caret's Edit Volume Attributes, and from manually looking for the AC), but none seem to give me accurate 
correspondence.  The orientation is LPI (within Caret)......the real volume name is series003.LEFT_HEM+orig.nii , but Caret 
detects it as series003.LEFT_HEM+orig.nii+tlrc.HEAD , so I put this is for its volume name.  Any suggestions would be great.....
I can also upload my volume and surface if you want.  

thanks
rishi 


> Date: Sun, 16 Mar 2008 12:01:18 -0500
> From: caret-users-request at brainvis.wustl.edu
> Subject: caret-users Digest, Vol 54, Issue 5
> To: caret-users at brainvis.wustl.edu

> Today's Topics:
> 
>    1. Re: Communicating with AFNI (David Van Essen)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sat, 15 Mar 2008 21:41:02 -0500
> From: David Van Essen <vanessen at brainvis.wustl.edu>
> Subject: Re: [caret-users] Communicating with AFNI
> To: "Caret, SureFit, and SuMS software users"
> 	<caret-users at brainvis.wustl.edu>
> Message-ID: <DFCB4CB2-6A1A-47EA-8BB8-A725BB422E39 at brainvis.wustl.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
> 
> Rishi,
> 
> John's matrix-related comments appear to be on track, based on my  
> superficial reading.  But I wanted in particular to follow up on his  
> comment about future support for Caret-AFNI communication.
> 
> We set this up quite a few years ago when Caret didn't handle volume  
> visualization.
> 
> Caret now has much more robust volume visualization capabilities,  
> including concurrent volume-surface visualization in different  
> window.  Consequently, it is very rare that I or others in my lab use  
> the Caret-AFNI linkage even when we are viewing AFNI volumes.
> 
> I recognize that AFNI has a lot of analysis tools that we don't even  
> attempt to emulate in Caret.  But is there something in the  
> visualization domain that makes a Caret-AFNI linkage especially useful  
> to you? (Or to others who might choose to chime in?)  Or had you just  
> not given much thought to trying surface-volume comparisons within  
> Caret?
> 
> The answer(s) may influence whether we preserve this feature in future  
> Caret releases.
> 
> David
> 
> 
> On Mar 14, 2008, at 11:44 AM, John Harwell wrote:
> >
> > AFNI must be started with "-yesplugouts".  Load the matrix file into  
> > Caret prior to attempting communication with AFNI.
> >
> > Be aware that this AFNI and FIV communication may be removed from  
> > future versions of Caret.
> >
> >
> >
> > On Mar 14, 2008, at 10:53 AM, Rishi Kalwani wrote:
> >
> >> Hi,
> >> I'm trying to use AFNI to communicate with my Caret Surface.....
> >> I'm told I need a transformation matrix file to do so.
> >> I'm want to use the volume I used to generate the surface.
> >> Anyway, I was wondering what the procedure is to communicate with  
> >> AFNI?
> >> thanks
> >> rishi
> >> Connect and share in new ways with Windows Live. Get it now!  
> >> _______________________________________________
> >> caret-users mailing list
> >> caret-users at brainvis.wustl.edu
> >> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
> >
> > _______________________________________________
> > caret-users mailing list
> > caret-users at brainvis.wustl.edu
> > http://pulvinar.wustl.edu/mailman/listinfo/caret-users
> 
> 
> ------------------------------
> 
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
> 
> 
> End of caret-users Digest, Vol 54, Issue 5
> ******************************************

_________________________________________________________________
Connect and share in new ways with Windows Live.
http://www.windowslive.com/share.html?ocid=TXT_TAGHM_Wave2_sharelife_012008
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brainvis.wustl.edu/pipermail/caret-users/attachments/20080317/e09906af/attachment-0001.html>


More information about the caret-users mailing list