[caret-users] Communicating with AFNI

John Harwell john at brainvis.wustl.edu
Fri Mar 14 11:44:20 CDT 2008


Rishi,


If I remember correctly, the matrix is needed to convert a caret  
fiducial surface coordinate into a voxel index and vice versa.  Listed  
below are matrices I dug up from an old tutorial data set ".matrix"  
file.  You will need to create a matrix for the Caret to AFNI  
communication to function.

BeginHeader
date 07 Nov 2003 13:12:44
comment
encoding ASCII
EndHeader
tag-transformation-matrix-file-version 2
tag-number-of-matrices 7
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 Human.colin.LR.TLRC-711-2B.111+orig.HEAD
tag-matrix-target-volume-dimensions 176 208 176
tag-matrix-fiducial-coord-name Human.colin.Cerebral.R.FIDUCIAL.TLRC. 
711-2B.71723.coord
tag-matrix-target-AC-coords 88 122 73
tag-matrix-begin
1.000000 0.000000 0.000000 88.000000
0.000000 1.000000 0.000000 122.000000
0.000000 0.000000 1.000000 73.000000
0.000000 0.000000 0.000000 1.000000
tag-matrix-name Colin AFNI tlrc via 711-2B
tag-matrix-comment must be in afni+tlrc view
tag-matrix-target-volume-name Human.colin.LR.TLRC-711-2B.111+tlrc.HEAD
tag-matrix-target-volume-dimensions 161 191 151
tag-matrix-fiducial-coord-name Human.colin.Cerebral.R.FIDUCIAL.TLRC. 
711-2B-afni.71723.coord
tag-matrix-target-AC-coords 80 80 65
tag-matrix-begin
-1.000000 0.000000 0.000000 80.000000
0.000000 -1.000000 0.000000 80.000000
0.000000 0.000000 1.000000 65.000000
0.000000 0.000000 0.000000 1.000000



Set "tag-matrix-target-volume-name" to the name of the anatomical  
volume loaded in AFNI.

Set "tag-matrix-target-volume-dimensions" to the dimensions of the  
volume file.

Set "tag-matrix-target-AC-coords" to the voxel indices of the anterior  
commissure in the volume file and should also be in the right column  
of the matrix.

Set "tag-matrix-fiducial-coord-name" to the name of the fiducial  
surface.

The "1.0" values in the matrix may need to be "-1.0" if the  
orientation of the volume is not LPI (surfaces in Caret are LPI).

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.

-----------------------------------
John Harwell
john at brainmap.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110



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!  
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