> We are conducting an analysis on anatomical MRI images, following the Good
> optimized protocol. We have a question about proper analysis of white
> matter.
>
> As part of the first segmentation during pre-processing, we understand that
> after segmenting our non-normalized images, we then extract a brain image
> and then use Imcalc, selecting the _seg1.img, _seg2.img, and brain_.img,
> and applying the formula (posted by John 7 Jan 2002) i1./(i1+i2+eps).*i3 to
> obtain cleaned up gray matter images. Then, we normalize these images to
> our study-specific gray matter template, and apply those normalization
> parameters to the orginal images.
I relatively recently figured out that selecting _seg1.img, _seg2.img, _seg3.img
and brain_.img, and entering i1./(i1+i2+i3+eps).*i4 gives slightly more
pleasing results.
>
> Our question is: As we understand, this only creates optimal gray matter
> parameters. Do we need to create separate white matter masked images? If
> so, is there a different optimized formula (for white matter masks) and
> images to select to apply this formula to?
You can clean up WM by selecting _seg1.img, _seg2.img, _seg3.img
and brain_.img, and entering i2./(i1+i2+i3+eps).*i4 .
>
> How do we obtain optimal normalization parameters for white matter and how
> do we apply these to the original images? Do we apply the gray matter sn3d
> files to the original images, and then the white to the same file, or do we
> create a separate file for white matter analysis?
See the recent email about "VBM analysis path questions" for a bit more info.
Best regards,
-John
--
Dr John Ashburner.
Functional Imaging Lab., 12 Queen Square, London WC1N 3BG, UK.
tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381
fax: +44 (0)20 78131420 http://www.fil.ion.ucl.ac.uk/~john
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