A magnetic resonance imaging system for acquiring magnetic resonance data (158, 168) from a subject within an imaging zone, wherein the magnetic resonance imaging system comprises: - a memory containing machine-executable instructions (180, 182, 184, 186, 188); - a processor for controlling magnetic resonance imaging system, wherein execution of the machine-executable instructions causes the processor to: - receive a baseline medical image of the subject, wherein the baseline medical image comprises image data descriptive of one or more internal structures of the subject; - receive a baseline scan geometry, wherein the baseline scan geometry comprises data descriptive of a baseline scan geometry relative to the one or more internal structures; - acquire survey magnetic resonance data from the subject by controlling the magnetic resonance imaging system with survey pulse sequence data, wherein the survey pulse sequence data comprises instructions for controlling the magnetic resonance imaging system to acquire magnetic resonance data descriptive of a three-dimensional volume of the subject according to a survey scan geometry; - reconstruct the survey magnetic resonance data into a three-dimensional survey image; - calculate location data by processing the three dimensional survey image with an organ detection algorithm, wherein the location data is descriptive of a target region that contains at least a portion of the one or more internal structures; and said target region corrsponds to a subregion in the survey image that is moveable with respect to its surrounding structure within the survey image; - assign a predefined region of interest to the three dimensional survey image using the location data; - calculate registration data by registering the baseline medical image to the three dimensional survey image using an image registration algorithm, wherein the three dimensional survey image comprises a first group of voxels that are within the predefined region of interest and a second group of voxels that are outside of the predefined region of interest, wherein the image registration algorithm assigns voxels within the first group of voxels a higher weighting than the second group of voxels, wherein the registration data is descriptive of a geometric transformation of the one or more internal structures in the baseline medical image to the three dimensional survey image; - calculate an updated scan geometry by transforming the survey scan geometry with the geometric transformation; and - acquire follow-up magnetic resonance data from the subject by controlling the magnetic resonance imaging system with follow-up pulse sequence data, wherein the follow-up pulse sequence data comprises instructions for controlling the magnetic resonance imaging system to acquire the follow-up magnetic resonance data using the updated scan geometry. - a memory containing machine-executable instructions (180, 182, 184, 186, 188); - a processor for controlling magnetic resonance imaging system, wherein execution of the machine-executable instructions causes the processor to: - receive a baseline medical image of the subject, wherein the baseline medical image comprises image data descriptive of one or more internal structures of the subject; - receive a baseline scan geometry, wherein the baseline scan geometry comprises data descriptive of a baseline scan geometry relative to the one or more internal structures; - acquire survey magnetic resonance data from the subject by controlling the magnetic resonance imaging system with survey pulse sequence data, wherein the survey pulse sequence data comprises instructions for controlling the magnetic resonance imaging system to acquire magnetic resonance data descriptive of a three-dimensional volume of the subject according to a survey scan geometry; - reconstruct the survey magnetic resonance data into a three-dimensional survey image; - calculate location data by processing the three dimensional survey image with an organ detection algorithm, wherein the location data is descriptive of a target region that contains at least a portion of the one or more internal structures; and said target region corrsponds to a subregion in the survey image that is moveable with respect to its surrounding structure within the survey image; - assign a predefined region of interest to the three dimensional survey image using the location data; - calculate registration data by registering the baseline medical image to the three dimensional survey image using an image registration algorithm, wherein the three dimensional survey image comprises a first group of voxels that are within the predefined region of interest and a second group of voxels that are outside of the predefined region of interest, wherein the image registration algorithm assigns voxels within the first group of voxels a higher weighting than the second group of voxels, wherein the registration data is descriptive of a geometric transformation of the one or more internal structures in the baseline medical image to the three dimensional survey image; - calculate an updated scan geometry by transforming the survey scan geometry with the geometric transformation; and - acquire follow-up magnetic resonance data from the subject by controlling the magnetic resonance imaging system with follow-up pulse sequence data, wherein the follow-up pulse sequence data comprises instructions for controlling the magnetic resonance imaging system to acquire the follow-up magnetic resonance data using the updated scan geometry.