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Hi,
When I segment brain CT images using mri_synthseg with the following command line:
mri_synthseg — $file_to_segment —o $output — robust —ct —threads 10 —vol FS_vol.csv —qc FS_qc.csv

I get segmentation errors concerning the cortex for many CCTs: e.g. some scattered patches of the contralateral right cortex are segmented/labeled as left cortex and vise versa. 
How can I avoid this error? I think the algorithm should be able to recognize the hemisphere and not scatter patches of left cortex within right cortex? 
When I use —parchment paper I in the same patients I get similar segmentation errors but different voxels that are segmented with errors.
Ho can I improve the segmentation and get at least correct segmentation of the hemispheres?
 
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PD Dr. med. Susanne Gellißen

Department of Diagnostic and Interventional Neuroradiology
University Medical Center Hamburg-Eppendorf 
Martinistraße 52, 20246 Hamburg
E-mail: s.siemonsen@uke.de







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