By infrared thermometers we can measure surface temperature of weld bead but how to measure temperature of weld nugget at a particular depth of weld cross section in friction stir welding.
You need to use thermocouples to measure the temperature variation, but for different location you can drill small holes on the desired locations and implant those thermocouples into these holes and data can be collected through data acquisition. Make sure the holes are close to the weld enough and the weld is passing close by not through, otherwise the thermocouples will be destroyed.
Using thermo-couple to measure temperature in nugget zone is challenging job as this zone undergoes severe plastic deformation during the joining process which may damage the contact type measuring device. So better depend on analytical/numerical estimation.