Hi Dana,
Something like this should do the trick (assuming all your siena directories end in _sienax and are in the same directory):
for sienadir in *_sienax
do
echo $sienadir $(cat $sienadir/report.sienax | awk '/VSCALING/ {print $2}’)
done
Cheers,
Eelke
> On 14 Oct 2015, at 22:58, Dana Wagshal <[log in to unmask]> wrote:
>
> Hi Eelke,
>
> Thank you so much for your reply. It was very helpful! My remaining question is how do I get the VSCALING value for every subject without having to open up an internet webpage? Is there a way to script this and get the VSCALING value?
>
> Best,
> Dana
>
> On Wed, Oct 14, 2015 at 3:18 AM, Eelke Visser <[log in to unmask]> wrote:
> Hi Dana,
>
> Using the T1_to_std_sub.mat file to find the scaling is probably not ideal, as that registration is optimised for the subcortical structures and doesn’t take most of the brain into account. A convenient way to get an estimate of head size related scaling is to run SIENAX (which uses avscale internally) on your scans. The VSCALING value in its log is inversely proportional to brain volume, which means that you can multiply the volume reported by fslstats by this value to get a normalised volume.
>
> Hope that helps!
>
> Cheers,
> Eelke
>
>
>
> > On 13 Oct 2015, at 19:43, Dana Wagshal <[log in to unmask]> wrote:
> >
> > Hi FSL group,
> >
> > I have run the steps in order to complete a volume analysis using FIRST. My last step was to use fslstats to get the volume (ex. fslstats lcaudate -V). However, the volume is in subject-specific T1 space. How do I get this value to be in standard space? I've read the archives and it seems that I should use the avscale command. However, I am a bit confused on the exact commands and how to get the end result that I can put into a stats program like SPSS.
> >
> > From my fslstats command, I get the volume from every subject (by using the 2nd number provided in the fslstats -V command) in T1 space. What are the exact commands to use avscale? I'm still unsure even after reading the usage...
> >
> > For every subject I have a file called T1_to_std_sub.mat, is this the file I should be using?
> >
> > ex. avscale T1_to_std_sub.mat
> >
> > If this is the correct usage, what is the number I should use to multiple the volume in T1 space to get it to standard space? Is it the number found in Average Scaling (ex. Average scaling = 1.11215)?
> >
> > Sorry for all the questions!!
> >
> > Best,
> > Dana
>
>
>
>
> --
> -Dana
