Dear all,
because of some regions in a special EPI scan that do most likely not
move like a rigid body, I would like to in- or exclude some parts of the
scanned functional volumes not to take part in the realigment
cost-function, eg to exclude thos voxels.
To do that, I am playing around with realigment in spm5, and was
wondering what exactly the 'weighting' field in the estimation options
for realigment is doing. I would guess it can simply modulate the
contribution of a voxel for the difference cost function that is
minimized in realigment, but I am not sure from the help text in the
SPM5 interface nor the manual. It states:
----
Weighting
The option of providing a weighting image to weight each voxel of the
reference image differently
when estimating the realignment parameters. The weights are proportional
to the inverses of the
standard deviations. For example, when there is a lot of extra-brain
motion - e.g., during speech,
or when there are serious artifacts in a particular region of the
images.
-------
Am I right that when I provide an image here with 1s for voxels that can
contribute to the cost function, and 0s when not, that I can realize
exclusion of voxels entering the cost function? The 'inverses of the
standard deviations' in the above make me little uncertain whether this
is the case.
Otherwise, I can of course simply mask out parts of the functional
images in a script before realigning, but the above seems more elegant
and less disk-space consuming.
Many thanks for any pointers, have a nice weekend,
Bas
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Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
Visiting : Heidelberglaan 100, 3584 CX Utrecht
Room B.01.1.03
Mail : Huispost B.01.206, P.O. Box 85500
3508 GA Utrecht, the Netherlands
Tel : +31 (0)88 7559609
Fax : +31 (0)88 7555443
E-mail : [log in to unmask]
Web : http://www.fmri.nl/people/bas.html
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