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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