Hello,
> 1. How to make a batch file for coregistration + segmentation of all the
> input T1 images?
> What I did was: make a batch file for coregistration of 1 T1 image to the
> MNI-space T1 template, and use a dependency to segment the output of the
> coregistration. The other input image names were put into the same batch
> file using a script
> Somewhere along the way, 'new segment' always crashes. With 'segment' it is
> (at least, was) possible to finish this step. Is it equivalent to use
> 'segment' instead and then do the DARTEL import step separately (instead of
> having the import step built-in with 'new segment')?
I'll have to leave the batching part to someone else. However, just
to make sure it's clear, using 'segment' + DARTEL import will be
different than 'new segment' because the tissue probability maps are
different (and probably more accurate) in 'new segment'. I.e. they
are equivalent in that you will end up with rc* images, but because
the segmentation routine isn't identical, you're going to end up with
different results.
> But is it a good idea to normalise to MNI space? Or is it better to warp the
> images to the DARTEL-created template instead?
When I've compared results in "DARTEL space" with those same results
put into MNI space they are extremely similar (as you'd expect).
Because having your results in MNI space greatly facilitates the
sharing of data and reporting of results, I think it's definitely a
good idea. (Note that normalizing to MNI uses the flow fields
generated during template creation, along with the parameters required
to get the template to MNI space, to bring each subject into MNI
space. So you're still gaining a lot of benefit from doing this
through DARTEL.)
Hope this helps!
Jonathan
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