Dear Jesper,
Thank you so much for your prompt and valuable advices.
We will try--biasres (from default 50,50,50 to 30,30,30: 20,20,20;
10,10,10) and --in&refpointlist.
As for --pointlistlambda=1, how can we modify it?
Change by order of 1 (e.g., =2, 3, 4) or by 10?
Many thanks again for your kind assistance.
Sincerely,
Riki
--
Riki Matsumoto M.D., Ph.D.
Department of Neurology
Kyoto University Graduate School of Medicine
Shogoin, Sakyo, Kyoto, JAPAN 606-8507
Tel: +81-(0)75-751-3772
Fax:+81-(0)75-751-9416 (for large transfer, use +81-(0)75-761-9780)
> It sounds like you have done most of the things I would recommend. The
> critical thing is that fnirt assumes that everything that is present
> in one image is present also in the other (though it may have a
> different size and shape). So e.g. if it finds a ventricle in one
> brain it expects to find one in the other as well.
>
> This assumption is of course not fulfilled when you have a pathology
> (e.g. a tumor) or some foreign object (electrode) in one of the images
> and not in the other. Our recommendation then is to mask these areas
> out using some suitable combination of --inmask and --refmask. And it
> sounds like you have already done that.
>
> Another possibility (which does not address your electrodes, but might
> help those intensity hot-spots) is to use a higher resolution for the
> bias-field. It will mean longer execution time, and may not work if it
> means that intensity and shape gets too strongly correlated. But it
> would be worth a try.
>
> Another thing you might try is to complement your data with a list of
> point correspondences. This is a hidden feature, that is quite
> untested, that might potentially help you. If you are able to manually
> identify unique points in both volumes you can put these in two text
> files, and that means that these points will serve as an anchor
> between the two volumes (and might prevent fnirt from doing silly
> things in that region).
>
> Let us say e.g. that you have managed to identify two points on the
> cortical surface in both volumes. You should then create a file with
> the points identified in the --ref file, e.g.
>
> ref_pl.txt contains
> 15 45 67
> 18 52 63
>
> and one for the --in file
> in_pl.txt contains
> 20 42 56
> 23 50 50
>
> when running fnirt you then specify these with
>
> fnirt --ref=.... ..... --refpointlist=ref_pl.txt
> --inpointlist=in_pl.txt
>
> These points are not "completely anchored", but rather have some
> slack. The amount of slack is given by the
>
> --pointlistlambda
>
> parameter. The default is --pointlistlambda=1 , but you may wish to
> experiment with it.
>
> Also, please note that there is a reason I hid this option for the
> release. I need to do lots more testing of it, and there is a risk you
> may encounter problems with it.
>
> Good luck Jesper
>
>
>
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