Hi FSL'ers,
I'm new to FSL (really liking it so far). I'm hoping for advice on the best
approach to combining two MPRAGE images from the same subject. This is for
100+ subjects, and so I will script it. the idea is to end up with one
higher-quality image to use in structural analyses. one image is from the
start of the scan session, and the other from the end (~1.25 hours later).
flirt seems like the way to go, so I searched the archives and the flirt
lecture notes from the web (pdf), but did not see something on combining
MPRAGES. my apologies if I missed it.
one question is:
- is it always better to combine two images? presumably there could be
pathological cases (e.g., lots of movement resulting in a blurry image)
where a single good MPRAGE is better than combining one good and one bad --
so is there a way to tell that you are in such a situation (especially for a
script to tell this)? just inspect afterwards?
using flirt seems straightforward:
- prior to flirt, run bet -B on each image (= my interpretation of flirt
lecture slide #45). but maybe for having the same sequence, the non-brain
stuff will actually help the alignment? and maybe doing bet on the combined
image will give a better extraction (for having a higher-quality input)?
- just pick one image to use as the reference, "better quality" should be
moot with 2 MPRAGEs (except in pathological cases)
- a rigid body 6-parameter model seems fine because the images are from the
same subject, same scanner, same day. is there any possible advantage to
more df for my situation?
- search option = "already virtually aligned" is probably fine
- cost function: correlation ratio is the default in the GUI. however, I've
heard that normalized mutual information is very good, in particular is
robust to small non-brain bits left over from brain extraction. any reason
not to use NMI (especially if I do bet prior to flirt)?
- trilinear interpolation (= default) -- any advantage to sinc?
thanks much,
--Jeremy
/*-------------------------------------------------------------
Jeremy R. Gray, PhD
Assistant Professor, Yale University
Dept. of Psychology & Interdepartmental Neuroscience Program
mail Box 208205, New Haven, CT 06520-8205 USA
office SSS 212
http://maps.google.com/maps?q=1+Prospect+St,New+Haven
phone 203-432-9615 (office)
fax 203-432-7172 (include Attn J. Gray)
web http://www.yale.edu/scan/
-------------------------------------------------------------*/
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