Hi,
If you determine what command line you need for a single subject (e.g. by running the GUI and looking at the commands it prints in the terminal), then you can just write a simple script that loops over directories for each subject. If you keep the naming of the images within each directory the same then the script can be very simple. Something along these lines would do the job:
for dn in subj* ; do
cd $dn
… bedpostx or probtrackx call goes here ...
cd ..
done
Where the "subj*" needs to be replaced with a suitable wildmask that fits your directory names (this one would match any directories that started with the name "subj" - like subj0001, subj0002, or anything starting with subj - so just use whatever suits your own naming conventions here). The middle line (in between … and …) needs to be replaced with a specific call.
Note that the "cd .." line should be left exactly as it is.
I hope this helps.
All the best,
Mark
On 3 Sep 2014, at 04:20, Emily Louise Belleau <[log in to unmask]> wrote:
>
> ________________________________________
>
> Hello FSL experts,
>
> I had a question about where to begin in terms of batch processing probtractx on around 80 subjects.
>
> I am new to FSL and am not sure where to begin.
>
> I planned examine connections between the basolateral amygdala (seed mask) to the vmpfc (waypoint and termination mask).
>
> I plan to use all of the default settings.
>
> *All preprocessing stages that need to be done prior to probtrackx are already done including bedpost.
>
> Any guidance you can give me would be greatly appreciated!
>
> Emily
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