Hello Donna,
yes, I see the trade-offs, and I have just tried registering the
surfaces from the T1s of the subjects onto those from the group-average
T1: although the main landmarks are there, the resulting surfaces are
horrible!
The way I see it, what is important is that I check the projections of
the functionals onto the average of the surfaces of my subjects,
whichever target I might choose for the spherical registration.
Thank you for your time and for your pro bono tutoring :-)
Bruno
On 15/10/2010 11:23 AM, Donna Dierker wrote:
> On 10/14/2010 03:29 PM, Bruno L. Giordano wrote:
>> Hi Donna,
>>
>>>> 1. create a target surface from the SPM-normalized T1s of each of the
>>>> participants: this is not a very nice representation, but it shows
>>>> very clear landmarks (with the possible exception of the ventral
>>>> medial wall);
>>> So far, so good. What software will you use to generate the surfaces?
>> My description was incomplete: I meant average the
>> participant-specific SPM-normalized T1s to create a group-average T1.
>> Then create a target surface by segmenting this group T1 with Caret.
>> This surface will obviously look bad. However, it still has each of
>> the default landmarks very clear. This target surface will be improved
>> at point 3.
> Segmenting group averaged MRI is usually a bad idea.
>>>> 2. project the surfaces of the participants (derived from
>>>> SPM-normalized T1s) onto this target surface;
>>> This isn't really clear. As best I can discern, you mean register your
>>> subjects to the PALS-B12 target atlas, at which time your various coord
>>> files, including fiducial/midthickness coord files, will get resampled
>>> onto the PALS-B12 73730 standard mesh.
>> See above.
>>>> 3. create a new improved target surface by averaging those coming out
>>>> from 2. (eventually include the additional temporal landmarks at this
>>>> point and not at 1.).
>>> Why? What is your motivation for creating a customized target, instead
>>> of using PALS-B12? What is different about your subjects?
>> My thought is that by using a target surface that actually comes out
>> from my subjects the quality of the functional-to-surface mapping will
>> be improved, especially if I do the points 4-6. below:
>>
>>>> 4. project the surfaces of the participants used at 2. on the new
>>>> target;
>>>> 5. average surfaces coming out at 4;
>>>> 6. project my functionals (group results) onto the average surface
>>>> from 5.
> No, I am not convinced you will significantly improve your outcome this way.
>
> If I understand you correctly -- and I'm not sure I do -- you still plan
> to segment your individuals and register their surfaces to some target.
>
> The question is what the target should be. I remain unconvinced that
> there is benefit to be gained by generating this customized target. I
> don't think tightened correspondence across nodes will offset the loss
> of benefit of using the PALS-B12 target (e.g., availability of several
> published parcellation schemes, borders, fMRI results from published
> studies, left-right correspondence).
>
> Now if you were not segmenting/registering your subjects, but rather
> just mapping their group results on some average fiducial surface, then
> I do acknowledge that a surface coming out of step 1 above would be
> closer to your subjects than the available PALS-B12 surfaces. But then
> your results would be less comparable to other studies than ones that
> mapped to these standard average fiducial surfaces. You see the trade-offs?
>
> Honestly, I don't think it's worth the effort, but I encourage my
> colleagues to speak up if they disagree.
>> Please correct me if I'm wrong. Thank you again,
>>
>> Bruno
> .
>
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