PT is often about trading short term pain for long term improvement.
PT is also about communication, with therapist and patient working together toward the goal. The therapist has no way of know what the patient feels except by listening to the patient. Likewise the patient has no way of knowing what the therapist is looking for or expects except unless the therapist explains his thinking. Without good 2-way communication, decent PT is nearly impossible.
In your shoes, I'd go back to the physician with your issues, and him what he thinks, and if another therapist can be assigned to your case.
BTW- I would have gone back to the primary physician long before things came to a head.
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