Hi Eekle,
Thanks for your helpful reply.
We generated the probability maps from atlas by non-linear registration and it is hard to form the transform matrix as specified by the default ident.mat.
In the manual, the sentence "-P <file> or --Prior use prior probability maps at all segmentation stages" seems that the prior probability maps is not only used for initialisation.
My idea is that can we set a weighting term to weight the prior maps in the whole segmentation procedure?
Thanks,
Zheng
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Eelke Visser
Sent: Wednesday, September 30, 2015 3:33 AM
To: [log in to unmask]
Subject: Re: [FSL] fast segmentation
Hi Zheng,
To use prior images you need to specify both the -a and -A options:
fast -a prior2input.mat -A prior_prob_0 prior_prob_1 prior_prob_2 [-P] <other options>
The -a option specifies the affine transformation (from FLIRT) that registers the priors to the input image. If you have already registered them, you can specify $FSLDIR/etc/flirtsch/ident.mat for the matrix. The optional -P option tells fast to use the priors in the final segmentation as well; by default it only uses them for initialisation (see the manual for some more details).
You can specify the prior images in any order - the order of the outputs will correspond to the input order.
Cheers,
Eelke
> On 29 Sep 2015, at 22:50, Zheng Liu <[log in to unmask]> wrote:
>
> Hello:
>
>
>
> How to input the prior probability maps in fast command?
>
> For example:
>
> fast -t 1 -n 3 -H 0 -I 4 -l 20.0 -g -p -o output-withprior input.nii.gz -P prior_prob_0.nii.gz prior_prob_1.nii.gz prior_prob_2.nii.gz
>
> that’s correct? And the order of probability maps is CSF, GM and WM?
>
>
>
> Thanks,
>
> Zheng
>
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