Hi,
In the new version of FSL (4.1.4) you can simply use
run_first_all which will segment all structures for you
and also apply a boundary correction that takes into
account multiple structures, avoiding all overlaps. It
also does the registration too.
This is actually much simpler to use than before and the
documentation has been substantially expanded. So
update to 4.1.4 (if you haven't already) and try run_first_all
All the best,
Mark
On 22 Jun 2009, at 14:09, Nick Papanikolaou wrote:
> Dear All,
>
> I'm trying to quantify the volumes of different subcortical
> structures. Currently, I'm using
> the following to quantify i.e. hippocampal volume:
>
>
> first_flirt t1.nii.gz t1_std_sub -d
>
> run_first -i t1 -t t1_std_sub.mat -n 50 -o t1_l_hipp_n50 -v -m
> /usr/local/fsl/data/first/models_336_bin/l_hipp_bin.bmv
>
> first_utils --singleBoundaryCorr -i t1_l_hipp_n50 -r t1 -p 3 -o
> t1_l_hipp_n50_bcorr_p3
>
> fslstats t1_l_hipp_n50_bcorr_p3.nii.gz -V
>
> I was wondering if its possible and how to do the previous task for
> different structures
> (i.e. amygdala, putamen, pallidus ...) simultaneously and not its
> one individually.
>
> Thank you in advance.
>
> Nikos
>
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