A Phase II Study of Intensity Modulated Total Marrow Irradiation (IM-TMI) in Addition to Myeloablative Fludarabine/Busulfan and Post-Transplant Cyclophosphamide (PTCY) for Fully Human Leukocyte Antigen (HLA)-Matched and Partially-HLA Mismatched Allogeneic Transplantation Patients With High-Risk AML, CML, and MDS

Inclusion Criteria: * 1\. Age 18-65 years. * 2\. Patients with CML, AML, or MDS who meet one of the following criteria: 2a. Relapsed or refractory AML (including AML in CR2) 2b. Poor-risk AML in first remission, with remission defined as \<5% bone marrow blasts morphologically: * AML arising from MDS, a myeloproliferative disorder, or secondary AML * Poor risk molecular features according to Leukemia Net including ASXL1, BCOR, EZH2, RUNX1, SF3B1, SRSF2, STAG2, U2AF1, and/or ZRSR2 * Poor-risk cytogenetics: Monosomal karyotype, complex karyotype (\> 3 abnormalities), inv (3), t(3;3), t(6;9), MLL rearrangement with the exception of t(9;11), or abnormalities of chromosome 5 or 7. 2c. Primary refractory disease 2d. MDS with at least one of the following poor-risk features: * Poor-risk cytogenetics including 3q abnormalities, 7/7q minus or complex cytogenetics (\>3 abnormalities). * Current or previous INT-2 or high IPSS score. * Treatment-related MDS. * MDS diagnosed before the age of 21 years. * Progression on or lack of response to standard DNA-methyltransferase inhibitor therapy. * Life-threatening cytopenias, including those requiring regular PRBC or platelet transfusions. 2e. CML with a history of accelerated or blast phase. Exclusion Criteria: * 1\. Presence of significant co-morbidity as shown by: * 1a. Left ventricular ejection fraction \< 50% * 2b. Creatinine clearance \<30ml/min. * 3c. Bilirubin \> 2.0 mg/dL (unless due to Gilbert's syndrome or hemolysis), and ALT and AST \> 5 x ULN. * 4d. FEV1 and FVC \< 50% of predicted or DLCO \<50% of predicted once corrected for anemia. * 5e. Karnofsky score \<70 * 6f. Active viral hepatitis or HIV infection. * 7g. Cirrhosis. * 2\. Pregnancy or breast feeding * 3\. Patients unable to sign informed consent. * 4\. Patients previously received radiation to \>20% of bone marrow-containing areas.