Hi Todd,
I think something like this should work:
*fsl2ascii ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz
~/MNI152_T1_2mm_brain.txt*
*cat ~/MNI152_T1_2mm_brain.txt00000 | tr " " "\n" | awk '$1 != 0 && $1 !=""
{print $1}' | sort > ~/MNI152_T1_2mm_brain_sorted.txt*
*head -n 100 ~/MNI152_T1_2mm_brain_sorted.txt*
All the best,
Anderson
On 7 December 2016 at 15:51, Todd Thompson <[log in to unmask]> wrote:
> Thanks, Anderson. It seems like a similar approach (count the number
> of non-zero voxels, figure out the percentage you want using simple
> math, threshold). It doesn't solve my wanting *exactly* <n> voxels,
> unfortunately, so it sounds like Matlab/Python are going to be
> required after all.
>
> Perhaps this could be an fslmaths feature request? It seems like a
> fairly common task to run something like MVPA on the top <x> voxels of
> an ROI.
>
> Thanks again,
> Todd
>
>
> On Wed, Dec 7, 2016 at 2:56 AM, Anderson M. Winkler
> <[log in to unmask]> wrote:
> > Hi Todd,
> >
> > The thread in the link below, from the list archive, is for a different
> but
> > related question. Perhaps it could give some ideas with fsl2ascii and/or
> > -p/-P in fslstats, have a look...
> >
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;68f60c58.1605
> >
> > All the best,
> >
> > Anderson
> >
> >
> > On 6 December 2016 at 16:58, Todd Thompson <[log in to unmask]> wrote:
> >>
> >> I'm trying to extract the top 100 voxels for each subject in a group
> >> from a particular contrast, and I'm wondering what the best way of
> >> doing that is. It seems like an fslmaths-y operation, but I don't see
> >> an obvious flag to use.
> >>
> >> The best I can come up with is doing something like:
> >> %get number of non-zero voxels
> >> fslstats cope.nii -V
> >>
> >> %Do some math: 100/NumVoxels = DesiredPercent
> >> fslmaths cope.nii -thrP $DesiredPercent output.nii
> >>
> >> And now I have an output image that will contain my voxels of interest.
> >>
> >> Two questions:
> >> 1) Is this really the right way to do this?
> >> 2) If I want exactly 100 voxels and there are voxels with duplicate
> >> values in e.g., voxel positions 95-105, this could lead to an unequal
> >> number of selected voxels per subject. Ideally, I'd end up with
> >> exactly 100 voxels where ties are broken in an arbitrary fashion. Can
> >> you see any way to do this with FSL tools?
> >>
> >> Thanks so much!
> >> Todd
> >
> >
>
