A magnetic resonance apparatus which acquires navigator signals generated from a navigator region including a first portion and a second portion, the navigator signals acquired using a coil having a plurality of channels, is provided. The magnetic resonance apparatus includes a scan unit configured to execute a first navigator sequence for acquiring first navigator signals generated from the navigator region, a profile generating unit configured to generate first profiles each including position information on the first portion for every channel, a determining unit configured to determine correlations between the first profiles and a template, and a selecting unit configured to select each channel used to acquire the position information on the first portion based on the correlations.