You're right that all_FA (and all_MD or all_ADC etc when you've run tbss_non_fa) may contain the values you need but if you want to look at the *skeleton* values that were actually used in the randomise calculation then you need all_FA_skeletonised (all_MD_skeletonised etc).

As you'll see if you open the files up in fslview they're 4D files with the 4th dimension being subject in (usually) alphabetical order. All_FA.nii.gz contains the FA maps warped into MNI space, and all_FA_skeletonised contains the skeleton values for each person in MNI space.

You could use some combination of fslmaths, fslsplit, fslstats or fslmeants to apply a mask and then get the mean values within those masks. Type each command without any arguments to get their usage.

I think fslmeants is probably your easiest bet:

For example: If you wanted to get the mean FA from the tbss skeleton within a mask of the corpus callosum (made by thresholding the appropriate file in $FSLDIR/data/atlases/... and called corpus_callosum_mask.nii.gz) you could type:

fslmeants -i all_FA_skeletonised.nii.gz -m corpus_callosum_mask.nii.gz -o mean_values_file.txt

I hope this helps!
Kx

On Thu, Jan 2, 2014 at 12:08 AM, charlie Leger <[log in to unmask]> wrote:

I would like to create a histogram and perhaps boxplot of TBSS FA ( and ADC) data. It seems the all_FA data might supply the frequency distribution data but I am uncertain how to proceed.

I would like to use R (statistics) to develop the graphs; I should be able to create masks of the FA and ADC data from which frequency distributions can be made.

As I have only a basic understanding of TBSS, any recommendations would be much appreciated.

Thank you

--
Kirstie Whitaker, PhD
Research Associate

tel: +44 7583 535 307

Department of Psychiatry
University of Cambridge
Herchel Smith Building
Robinson Way
Cambridge CB2 0SZ