Dear VBM'ers,
I am doing a VBM-type analysis and trying to set it up using DARTEL. So
far with varying degree of success, which is probably due to ignorance..
Should it be obvious
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')?
2. How to normalise the images?
In John's DARTEL guide
http://www.fil.ion.ucl.ac.uk/~john/misc/dartel_guide.pdf, The steps for
a group of structural images were
1. check reg (or coregister to MNI in my case)
2. segment
3. DARTEL initial import
4. DARTEL create template
5. DARTEL create warped
But in the VBM tutorial 'notes of the Edinburgh VBM class'
http://www.fil.ion.ucl.ac.uk/~john/misc/VBMclass10.pdf the procedure is:
1. check reg (same)
2. new segment (different)
3. DARTEL create template (same)
4. normalise to MNI (different)
One of the differences between 'segment' and 'new segment' is that it
creates the files that 'initial import' would otherwise create, so that
makes sense.
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?
Many thanks
Alle Meije Wink
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