Dear Mr. Philipp:
> 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.
I understand that some scholars used an explicit threshold such as 0.3 to
control for areas, is there a reference for how and why such a threshold
should be used?
> Not mentioned, but probably clear anyway: you should use the "modulation"
> option.
As the end result of the preprocessing of DARTEL are smwc1.nii files, which
I think to be normalized, modulated and smoothed files, where in the process
should I use "modulation" you mentioned?
Thank you again for you help!
Lin Yun
--------------------------------------------------
From: "Saemann Philipp" <[log in to unmask]>
Sent: Wednesday, March 31, 2010 3:02 PM
To: <[log in to unmask]>
Subject: Re: [SPM] A practical VBM study workflow and doubts
> 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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