Apologies, absolutely correct. My code would give the sum of all voxels
values regardless of value (in contrast to what I claimed), using capital -M
and -V would give sum all non-zero voxels and Tibor's code would actually
solve the problem as stated rather than something else entirely!
2011/7/28 Auer, Tibor MD. Ph.D. <[log in to unmask]>
> You need the threshold, if you want only the POSITIVE voxels.
>
>
>
> Auer, Tibor M.D. Ph.D.
>
> Biomedizinische NMR Forschungs GmbH
>
> am Max-Planck Institut für Biophysikalische Chemie
>
> Am Fassberg 11
>
> 37077 Göttingen
>
> Germany
>
> Phone/Work: +49-(0)551-201-1725
>
> Mobile: +49-(0)176-8012-7921
>
> E-Mail: [log in to unmask] <[log in to unmask]>
>
>
>
> *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On
> Behalf Of *Andrew Lawrence
> *Sent:* Thursday, July 28, 2011 5:20 PM
>
> *To:* [log in to unmask]
> *Subject:* Re: [FSL] fsl_tools
>
>
>
>
>
> Here's the same in csh using dc in case you prefer your calculations
> reverse polish :)
>
> lowercase -m and -v give stats for non-zero voxels without setting the
> threshold.
>
>
>
> set a = `fslstats image.nii.gz -m`
>
> set b = `fslstats image.nii.gz -v`
>
> set sum = `echo "${a} ${b[1]} * p" | dc`
>
>
>
>
>
> On 28 July 2011 16:12, Auer, Tibor MD. Ph.D. <[log in to unmask]> wrote:
>
> Sorry, there is one more modification (the previous will give you the sum
> of non-zeros):
>
> voxmean=$(fslstats img -l 0 -M);
> voxnum=$(fslstats img -l 0 -V | awk '{print $1}');
>
>
> voxsum=$(echo "$voxmean*$voxnum" | bc);
>
> Auer, Tibor M.D. Ph.D.
> Biomedizinische NMR Forschungs GmbH
> am Max-Planck Institut für Biophysikalische Chemie
> Am Fassberg 11
> 37077 Göttingen
> Germany
> Phone/Work: +49-(0)551-201-1725
> Mobile: +49-(0)176-8012-7921
> E-Mail: [log in to unmask]
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Gabor Perlaki
>
> Sent: Thursday, July 28, 2011 5:11 PM
> To: [log in to unmask]
>
> Subject: Re: [FSL] fsl_tools
>
> Thank you!
>
>
>
