thanks Peter, sounds very promising.
On Mar 8, 2008, at 10:59 AM, Peter Kochunov wrote:
> Jeremy
>
> You might want to check out this paper.
> http://www.ncbi.nlm.nih.gov/pubmed/16628607?
> ordinalpos=10&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.P
> ubmed_RVDocSum
>
> We routinly average up 7-8 MPRAGE studies in order to reduce motion
> in the high-res anatomical images.
> You can judge the quality of the individual segments by running a
> histogram analysis on them
> pk
>
> ----- Original Message ----- From: "Jeremy R. Gray"
> <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Friday, March 07, 2008 11:13 PM
> Subject: [FSL] combine two MPRAGEs?
>
>
> 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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