For some reason, this isn't entirely working for me. I put the files
into the directory I want to use and set avg152T1_ana as the anatomy
(Switch Anatomy). It makes the brain look different and the
coordinates look like Talairach coordinates. So far, so good. Also,
the top of the AFNI screen shows avg152T1_ana+tlrc.
But, when I try to use my functional data zstat1.hdr, the computer
beeps a couple of times (no text error messages) and the brain and
coordinates change to how they used to look. Also, the top of the AFNI
screen says avg152T1_ana+orig & zstat1.hdr+orig.
My assumption is that I need to somehow tell my functional data to warp
along with the anatomy. The warp on demand buttons are depressed for
both the anatomy and the functional images. And, I can click back and
forth between the original and talairach views, but it would make more
sense to get the functional data into the other space. Any ideas on
this?
Also, I haven't moved to using the AFNI TTatlas+tlrc to extract ROI's
yet. Have you done this? What is the sequence of steps? And, doesn't
this also require moving my data from +orig to +tlrc?
Darren
On Monday, June 23, 2003, at 04:36 PM, Edward Vessel wrote:
> Hi Darren & others ...
>
> I posted another solution to this issue on here a while ago:
>
> I created an AFNI version of the avg152 standard which ignores the
> normal afni
> coordinate conventions but instead uses the FSL standard brain
> conventions.
> Then, I marked the acpc and tlrc markers on this brain. By putting
> this
> brain (or a link) in any directory that has analyze files registered
> to the
> avg152 brain, I can now just click on the 'tlrc' button and view the
> analyze
> files in tlrc space, or at least something close.
>
> Go to
>
> ftp://geon.usc.edu/avg152T1_ana/
>
> to download the files.
>
> From: Darren Schreiber <[log in to unmask]>
>> Subject: Re: View each voxel and region
>>
>> I am struggling with this same problem currently. AFNI has the data
>> from the Talairach data imported as a functional image
>> (http://afni.nimh.nih.gov/afni/ttatlas.html) that can easily be used
>> to
>> extract data if your image is in the +tlrc space. Unfortunately, the
>> coordinate system for the data coming out of FSL doesn't match the
>> +tlrc coordinate system. At the FSL course, there was talk about
>> coordination between the AFNI and FSL folks to resolve the issue. I
>> am
>> not sure what progress was made, perhaps Steve can illuminate this.
>> It
>> seems to me that there would be great value from such a coordination
>> because then everyone who face Wei's problem (like me) could have an
>> elegant solution.
>>
>> I am going to try a less elegant solution, but I think one that is a
>> bit easier than Joe's proposal. I can view the TTatlas+tlrc image in
>> one instance of AFNI and I can view my FSL data in another instance of
>> AFNI (click "new" on the first AFNI window). So, I am going to use
>> the
>> plugin "Draw Dataset" to try to manually replicate the image of the
>> amygdala slice by slice using the TTatlas+tlrc as a reference. I
>> think
>> this will be easier than Joe's solution since there will be a visual
>> image to work with as well.
>
> But, I really think this would be a good thing to coordinate between
> AFNI and FSL
>
> --
> Ed Vessel
> U. of Southern California [log in to unmask]
> Dept. of Neuroscience
> HNB, 3641 Watt Way http://geon.usc.edu/~vessel
> Los Angeles, CA 90089-2520
> (213) 740-6102
>
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