Fujifilm X-T1 IR has a 16.0MP APS-C (23.6 x 15.6 mm ) sized CMOS sensor and features EXR Processor II processor. On the other hand, Sigma Quattro has a 29.0MP APS-C (23.5 x 15.6 mm ) sized CMOS (Foveon X3) sensor and features Dual TRUE III processor. Sigma Quattro's sensor provides 13MP more than Fujifilm X-T1 IR's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Another difference between these two cameras is that Fujifilm X-T1 IR's sensor lacks anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moire occurring in certain scenes.
Below you can see the X-T1 IR and Quattro sensor size comparison.
Fujifilm X-T1 IR and Sigma Quattro have almost the same sensor size so none of them has any significant advantage over other in this area.