John,
Questions:
So I have a nicer higher res T2 image for structual analysis. I want to
put my function results on top of that. I do the co-register. However,
do I really need to do the reslice? What does that buy my?
I want to have SPM take my higher res T2 and transform that to
correspond to my functional data. When I do the co-register I am asked a
series of questions:
1) Target image type
2) Object image type
3) pick target image
4) pick object image
5) pick other images.
For 1) I select T2 (for another study I picked T1).
For 2) I select T2
For 3) I point to the high res T2 (or the T1 as appropriate)
For 4) Do I point to the first functional image or to all of the
functional images?
For 5) I have no idea what "other" is. If in 4 I point to just 1 image
do I then point to the rest?
And if I don't reslice then what have I lost? That is, is the
co-registration calculation something that can be used later without
reslicing?
A question I also have is this, since I have done realignment, should
the co-registration actually calculate the co-registration parameters by
comparing the T2 structural to one functional and then apply this
calculation to the rest of the functional images?
In a sense I would actually like to save time by having the structural
T2 be resliced instead of the functional. To do this would I switch the
roles of target and object? And still the question lingers what is
"other" referring to?
Finally, does co-registration buy me anything with respect to the
statistical analysis? Does SPM discriminate between grey, white and CSF
when the probabilities of activation are being calculated? Or is
co-registration just for the purpose of presentation? (I presume the
same with normalization).
Also, how long should this take, that is the co-reg and re-slice? The
process seemed to be wanting to reslice the full set of our images (460
of them) and would also seem to take about 100 hours. Thus, I stopped
the process until I get the answers to these questions.
Maybe some of this is answered in SPM99b, but until we get the newMatLab
we are in SPM96 Land.
Finally, you wrote to me the other day:
>Be careful when you register structural images with distorted
functional
>images. The registration is never that good (because of the
distortions).
>Personally, I prefer to see results superimposed on the functional
images
>themselves. This way you can see exactly where the activations have
arisen
>from (unless the functional images have been distortion corrected).
Is there some software about that can handle fixing these distortions? I
see via SPM mail that SPM99 can
"Try SPM99b. The spatial normalization is much more stable. If you
are
already using SPM99b, then you can decrease the amount of distortion by
increasing the amount of regularization via the "Defaults" button."
Maybe once we have that installed here things will be more clear.
Finally, hopefully you did not already get this email yesterday. I
thought I sent it out and yet I see no evidence on my side that it went.
Thanks,
Robert
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