New atlases, update to autolabel, coreg with mask

[dtxe]

Addition of new atlas files, updates to the autolabel.py script for better handling of anisotropic voxels, and improvements to the electrode detection and labeling process.

Atlas Files Addition:

• Added new atlas files HCP-MMP1_cortices.xml, HCP-MMP1_cortices_1mm.nii.txt, and HCP-MMP1_on_MNI152_ICBM2009a_nlin.txt with detailed labels and coordinates for various brain regions. [1] [2] [3]

autolabel.py Script Enhancements:

• Changed the default CT value threshold for electrode detection from 2500 to 2000.
• Added handling for anisotropic voxels by upsampling to isotropic resolution, ensuring more accurate processing of CT images. [1] [2]
• Improved electrode detection and labeling process, including handling cases where no electrodes are detected and ensuring proper coordinate transformation. [1] [2] [3] [4] [5]
• Adjusted visualization parameters for better clarity in volume rendering.

Additional Argument in coreg.py:

• Added a new argument --inmask_mri to the pipeline_full function for specifying the path to the brain mask in MRI space.