This is a prospective randomized controlled feasibility study to determine whether navigation guided repetitive transcranial magnetic stimulation (rTMS) to the healthy hemisphere in patients with subacute stroke has a beneficial effect when given concurrently with task-oriented motor rehabilitation of the arm and hand. Navigation guided rTMS requires a structural MRI scan for targeting stimulation and therefore structural MRI will be performed on all subjects. In addition the study intends to determine whether measures of motor tract integrity (MTI) assessed by navigated brain stimulation (NBS) and MRI diffusion tensor imaging can be used to clarify prognosis of motor recovery and to monitor progress with rehabilitation. 30 subjects with ischemic or hemorrhagic stroke 3-9 months prior to enrollment and with residual upper limb hemiplegia will be randomized to receive either 1 Hz rTMS to the contralesional hemisphere for 30 minutes 3 times a week for 6 weeks along with rehabilitation therapy or sham rTMS to the contralesional hemisphere for 30 minutes 3 times a week for 6 weeks along with rehabilitation therapy. Primary outcome is improvement on the Action Research Arm Test, a measure of arm and hand function in people with stroke. Outcomes will be measured immediately post treatment, and at 3 months and 6 months post treatment.