Hi Carlos,
> After reading about people not reslicing their realigned data, and incorporating their motion parameters in the spatial normalisation transform, I'm trying to do it.
This is generally a good idea since you do not have to reslice the data
twice. Note that you can not do this if you want to unwarp since
unwarping does not only use a linear transformation and can thus not be
fully described using a matfile only.
> Step 1. Reorient images using the display window.
I take it you do this to one scan and then apply the parameters to all
images.
> Step 2. Slice timing
> Step 3. Realign button:
> a. Which option: coregister and reslice
> b. Create what?... Mean image only
You could now do a "reslice only" using the mean as the target, which
ensures that all images ahve contributed to the target image for motion
correction. This is pretty optional, though.
> Step 4. Smooth the mean image
this should not be necessary since spatial normalization will smooth the
data as part of the process.
> Step 5. Spatial Normalisation
> a. 7th degree B-spline interpolation
> b. Template : EPI.mnc
> c. Source image: the smooth mean image from step 4
I would use the unsmoothed image here.
> Step 6. Smooth the normalised images.
... and analyze, publish and become famous :) Way to go!
Marko
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Marko Wilke (Dr.med./M.D.)
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Universitäts-Kinderklinik University Children's Hospital
Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
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