Dear Riki,
> 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?
A value of 1 should give you "fairly firmly anchored" points, whereas a
value of e.g. 0.1 would allow more leeway. If you have some way of being
certain about the points (e.g. if the represent some fiducial markers) you
could use 10 or even 100 to make sure they are mapped exactly on top of
each other.
I am afraid that is as much advice as I can give on that. This weight
(relative the sum-of-squared differences cost-function) is something I
will need to determine before I "unhide" the option.
Good Luck Jesper
>
>
>
>> 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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