Hello Lin,
Wrt your pipeline: acc. to the manual and own experiences with New Segment
SPM8, the
skull stripping step is not absolutely essential. You might also try direct
use
of the New Segment routine.
Step 5 - explicit brain mask: here, it always depends, how you generate
that mask.
You might also control the area analysed by the analysis threshold.
Not mentioned, but probably clear anyway: you should use the "modulation"
option.
Qrt your questions:
1. - The fact that still SPM5 is in these publications does not indicate,
that SPM8 is worse, is just the typial delay factor I guess.
2. - I am not sure here who recommends this exactly. Segment includes a
"cleaning" step, that basically is skull stripping; it also includes a bias
correction step. FSL not essentially needed here.
3. - If you search the mailbase - there are numerous links to scripts that
give you the total volumes. One example of many:
http://www.nmrgroup.ion.ucl.ac.uk/atrophy/index.html
best wishes,
Philipp
Max Planck Institute of Psychiatry
NMR Research Group
Kraepelinstr. 2-10
80804 Munich
Mail: [log in to unmask]
Phone: 0049-89-30622-413
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