mp2rage_skullstripping¶
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nighres.brain.
mp2rage_skullstripping
(second_inversion, t1_weighted=None, t1_map=None, skip_zero_values=True, topology_lut_dir=None, save_data=False, overwrite=False, output_dir=None, file_name=None)[source]¶ MP2RAGE skull stripping
Estimates a brain mask from MRI data acquired with the MP2RAGE sequence. At least a T1-weighted or a T1 map image is required
Parameters: - second_inversion (niimg) – Second inversion image derived from MP2RAGE sequence
- t1_weighted (niimg) – T1-weighted image derived from MP2RAGE sequence (also referred to as “uniform” image) At least one of t1_weighted and t1_map is required
- t1_map (niimg) – Quantitative T1 map image derived from MP2RAGE sequence At least one of t1_weighted and t1_map is required
- skip_zero_values (bool) – Ignores voxels with zero value (default is True)
- topology_lut_dir (str, optional) – Path to directory in which topology files are stored (default is stored in TOPOLOGY_LUT_DIR)
- save_data (bool) – Save output data to file (default is False)
- overwrite (bool) – Overwrite existing results (default is False)
- output_dir (str, optional) – Path to desired output directory, will be created if it doesn’t exist
- file_name (str, optional) – Desired base name for output files with file extension (suffixes will be added)
Returns: Dictionary collecting outputs under the following keys (suffix of output files in brackets)
- brain_mask (niimg): Binary brain mask (_strip-mask)
- inv2_masked (niimg): Masked second inversion imamge (_strip-inv2)
- t1w_masked (niimg): Masked T1-weighted image (_strip-t1w)
- t1map_masked (niimg): Masked T1 map (_strip-t1map)
Return type: Notes
Original Java module by Pierre-Louis Bazin. Details on the algorithm can be found in [1] and a presentation of the MP2RAGE sequence in [2]
References
[1] Bazin et al. (2014). A computational framework for ultra-high resolution cortical segmentation at 7 Tesla. DOI: 10.1016/j.neuroimage.2013.03.077 [2] Marques et al. (2010). MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field. DOI: 10.1016/j.neuroimage.2009.10.002