Hi Stella,
Using FreeSurfer v.s. AAL parcellations for connectome construction require a considerably different set of steps (and one wouldn’t typically ‘instruct’ FreeSurfer to use the AAL parcellation even if it’s technically possible, which I’m not sure if it is).
There’s really two separate steps of interest that you need to deal with:
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Getting the AAL template parcellation into subject space;
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If necessary, converting the AAL parcel indices so that they form a continuous set from 1 upwards.
The first step is dealt with using image registration tools; there’s been a couple of discussions on this forum regarding the appropriate steps here, this post is all I can find right now though. The second step is dealt with using labelconvert, and its order with respect to the first step shouldn’t really matter.
Cheers
Rob