Hi Dorit, The reason why the colors look off is that mri_aparc2aseg will automatically add 1000 for left cerebral cortex and add 2000 for right cerebral cortex. Therefore, for example, a left hemisphere voxel in network 5 will have a value of 1005 in your test.mgz. Here is my suggestion:
1. Find the indices of left/right cerebral cortex by extracting the voxels with a value of 3 or 42 in the subject's aseg. 2. Use those indices to mask out the voxels that are not cerebral cortex in your test.mgz file (i.e. set non cerebral cortical voxels to be 0). 3. For the cortical voxels, you need to subtract 1000 for those between 1000 and 2000; and subtract 2000 for those greater than 2000. Best, Jingwei
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