Hi Thushini,
Are you referring to making a group probabilistic tract map?
If so, you could threshold and binarise each subject’s tract map using fslmaths with the -thr <threshold> and -bin flags. Then you could average the binarised tract masks across the cohort to give the probabilistic map.
e.g. using 0.5 as a threshold (50% if the image is stored as the same way as the results from probtrackx)
fslmaths tract_map -thr 0.5 -bin tract_map_bin
for each subject and then average the tract_map_bin maps.
Hope this helps.
Thanks,
Shaun.
> On 16 Mar 2020, at 16:28, Thushini Manuweera <[log in to unmask]> wrote:
>
> Hello,
>
> I have generated probabilistic tractography maps using a different toolbox and now I would like to use fsl to create a group probabilistic map with a threshold set at greater than 50%(i.e.only allowing connecting fiber tracks present in at least half of the subjects to be displayed). However, I am a little confused about how I could do this using fsl, since I am not very familiar with the toolbox.
> Is the probabilistic map created by first binarizing each individual tractography and then taking the sum of the of the group, which is then thresholded? if so then what command would I use to apply the thresholding?
>
> I hope the question is clear. Any feedback will be greatly appreciated.
>
> Thank you,
> Thushini
>
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