[caret-users] Re: caret-afni linking

donna at pulvinar.wustl.edu donna at pulvinar.wustl.edu
Wed Oct 8 08:38:08 CDT 2003


Mark,

Also check your AFNI volume's orientation.  If it isn't LPI, then you
might be better off sweating the details of creating a .matrix file, which
really just contains the affine transform needed to convert the surface's
fiducial coordinates to the volume's voxel coordinates.  For example,
assuming your volume is RAI -- not LPI, then your affine transform would
look like this:

-1 0 0 xlate-x
0 -1 0 xlate-y
0 0  1 xlate-z
0 0  0 0

The xlate values (fourth column) might just be your [XYZ]min values from
your .params file, but if you've translated your surface to AC origin,
then they might vary.

See the .matrix file in each surface subdirectory in the colin atlas for
an example; the AFNI +tlrc view is RAI.

Donna

> Mark,
>
> The most likely situation is that your fiducial surface is not in
> register with the volume and that it needs to be translated by an
> appropriate amount.  For instance, if your fiducial surface is in the
> 'native' space for the cropped right hemisphere, and you are looking at
> the full brain volume in AFNI, then you will need to add an additional
> offset to compensate for the cropping.  This can be done using the
> Surface: Transform: Translate REF config option, then saving the
> translated fiducial surface by a new name (e.g.,
> <case>.R.FIDUCIAL.InNativeVolume.<nodenum>.coord).
>
> If your original fiducial surface has been translated to a center of
> gravity or AC-origin, then you need to use a different translation, but
> the basic concept is the same.
>
>
> The transformation  can also be done by creating, then loading an
> appropriate matrix file, which allows a single fiducial surface to be
> mapped to more than one volume.  This is done using Surface: Transform:
> Apply/Edit matrix.   I won't try to explain the details here; there's
> additional info on the Caret online help menu.
>
> David
>
> On Tuesday, October 7, 2003, at 01:37 PM, Mark A. Pinsk wrote:
>
>>
>> Hello, I'm attempting to link afni and caret, and for some reason the
>> alignment b/n the two programs is incorrect  (when I click on the
>> caret surface, the afni crosshairs fall way off the brain).  The
>> directions of the crosshairs seem accurate (ex: clikcing posterior on
>> surface moves afni crosshairs posterior also), they just aren't in
>> alignment.  It looks like the caret surface (RH) is too far inferior,
>> left, and posterior in comparison to the AFNI volume.
>>
>> I start afni -yesplugouts and load my surface volume and corresponding
>> functional map.
>> Then i start caret and load the fiducial and ellipsoid surfaces and
>> paint on the functional map.
>> Then i Connect to Volume Program, leave the defaults
>> (localhost/7955/8009/Request on) and click OK.
>> Now I select a Target Volume (the surface volume loaded into AFNI), I
>> set the dimensions (256,256,128), select the coord file (the fiducial
>> coord file), and I don't have a matrix file (not sure if that's the
>> problem).
>>
>> Am I doing something wrong?
>>
>>
>>
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