[caret-users] Target space

[Donna Dierker]

Hi Jackie,

See inline replies below.

Donna

On 08/29/2007 07:16 AM, Chuan-Chih Yang wrote:
> Dear list,
>
> I got a question about the selection of target space (mapping volumes onto
> surface). My attemp is to map the functional zstat.nii of FSL onto N27
> template by using caret. I found different target spaces that I can choose
> from in the 'atlas surface selection' window,
>   
I hope you have a good reason for selecting Colin as the target surface, 
rather than PALS_B12.
> in my case--- the zstat of individual in not yet normalized to any space,
> but the group zstat is already normalized to MNI 305,by FLIRT. I am
> wondering which target space and altas shall I choose, if I wanna normalze
> the zstat from FSL onto N27?
>   
We don't have a version of Colin that was normalized using FLIRT (linear 
affine), but we do have versions of colin in SPM99 and SPM2 space.  (See 
http://brainvis.wustl.edu/help/pals_volume_normalization for an 
explanation of how methods and spaces relate in our terminology.)  You 
could use one of these for your group results, but I'd really recommend 
using the PALS_B12 FLIRT surface as your mapping target for those group 
results.

For your non-normalized individual results, you really can't use any of 
our atlas targets -- colin or PALS_B12.  If you want to map the native 
individual results, you'll need to segment his/her structural volume and 
map to the individual's surface.
> Is there any difference between mapping the individual zstat and the group
> zstat from FSL onto N27? 
Absolutely:  Mapping individual results to colin -- even normalized 
results -- is a bad idea.  Even mapping normalized individual results to 
PALS_B12 surface isn't a great idea.  Mapping individual results to its 
own surface reconstruction is a good idea.

Mapping group results to colin is no longer recommended, because of the 
limitations inherent in a single subject target.  Colin has strange 
anatomy in some places that cause undesirable mapping results in some 
areas (e.g., left posterior STS and IPL).

Mapping group results to PALS_B12 is the recommended option.

If you're interested in seeing how the individual's results differ from 
the group's, then I can think of two ways to accomplish this, but please 
be advised that I'm not experienced in these kind of analyses, so I 
don't know if a reviewer would be happy with them:

* Normalize your individual to the same target used for your group 
results.  Compute the difference in volume-land.  Map the difference 
volume to the PALS_B12 FLIRT surface.  Consider using the MCW BrainFish 
algorithm.

* Normalize your individual to the same target used for your group 
results; reconstruct your individual's surface; map the individual zstat 
to the individual's surface; and register it to PALS_B12.  Map the group 
zstat to the PALS_B12 FLIRT surface.  Use Attributes: Metric: 
Mathematical Operations to subtract one from the other (or 
caret_command's new metric math, if you have the latest and greatest 
command line utility).

Either way, you're guaranteed to get lots of clusters of differences; 
however, I'm not sure how you'd establish significance criteria.  Any of 
the 12 Buckner subjects that contributed to PALS_B12 will have such 
clusters where its individual surface differs from the PALS_B12 group 
target (i.e., normal anatomical variability is pretty high in humans).
> (is there a availble N27 altas that is FLIRTed into
> MNI305 ? )
>   
No.  You may have a good reason for using Colin, but I'd like to know 
what it is.
> Thanks much for the help!
>
> Cheers,
> jackie
>
>  
>
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