Hemisphere Masking

Hemisphere masking is fairly simple. All you need is your n3_305_6p.mnc file and your 6p_mask file to start.

1. Load the above files in Display.
   Display 10232_n3_305_6p.mnc -label 10232_mask_6p.mnc
2. Re-save the file as 10232_mask_6p_lh.mnc, and start by masking only the left hemisphere on the coronal view. Leave out the cerebellum. Remember that the most important thing on which to focus is the medial border of each hemisphere. Lateral borders are less important.
3. To make for faster rough hemisphere masking, delete the middle slice in the sagittal view using space-F-T while placing your mouse over the mask. Then you can use space-F-T on the right side of the mnc to get rid of the entire right section.
4. When you are finished with the left side, you can create a temporary right mask by using both the full, whole mask, and the newly created left hemisphere mask. To do this, simply run mk_tmp_rh_mask.csh in the scripts directory, like so:
   % cd /cxfs/schizo/family_study/scripts
   % ./mk_tmp_rh_mask.csh 10232_
5. Load the temporary mask with the mnc file, remove cerebellar tissue, and clean up the mask to finish. You are now ready for object creation.
   % Display 10232_n3_305_6p.mnc -label tmp_10232_mask_6p_rh.mnc
6. Save the new right hemisphere mask as 10232_mask_6p_rh.mnc and delete the temporary file.

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