Hi Jack,
what you outlined looks fine. There is a more recent VBM toolbox but it
needs a 6-volume-TPM which the TOM8 toolbox does not generate. I am
working on a successor but it is not ready for deployment yet so for now
your best bet would probably be as you described. Instead of setting the
AC/PC manually, you can also use the "center of amss" approach in teh
VBM toolbox, or do a rough coregistration to template space.
The only other thing I noticed is you stated "using the fieldmap where
collected". If you have subjects with and without fieldmap, I would very
seriously consider not mixing them together. The obvious options are
leaving out those without or not using it in those where you have it.
You could conceivably also include a covariate but I would be worried
that this is not sufficient.
Cheers,
Marko
Jack Rogers wrote:
> Dear SPM-experts,
>
> I was hoping you could advise us on whether you deem the below pipeline
> to be appropriate for a large MRI study we are running with
> children/adolescents aged 9 - 18 who are prone to movement in the
> scanner (a large number of them have behavioural problems and
> co-morbidity with ADHD). I will not go in to details regarding movement
> parameters here. It is mainly the pre-processing that we would like
> advice on.
>
> 1. Creating voxel displacement maps (VDM’s) using the processed fieldmap.
> 2. Realignment (unwarping using the fieldmap where collected)
> 3. Co-registration of the realigned and unwarped EPI and T1 scans
> 4. Set Origin of each T1 scan to the AC/PC line (is this needed - not
> recommended? It has been useful in previous structural MRI analyses).
> 5. Normalisation using DARTEL:
> a) Create customised tissue probability maps (TPMs) using the
> ‘Template-O-Matic’ (TOM; Wilke et al., 2008).
> b) Segment T1 scan using the customized TPMs with VBM8 (VBM8 still the
> most current?)
> c) Create DARTEL Templates
> d) Normalise to MNI
> 6. Checking pre-processing and dealing with motion artefacts
>
> If anything is unclear of if more information regarding justification
> for any of the steps would be helpful then please do let me know.
> Many thanks in advance.
> Jack
>
>
>
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn/
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