Expanding voxelwise with atlas based ICC

Adding ROI-based ICC calculations integrated with Nilearns datasets.

brain_icc.roi_icc(multisession_list, type_atlas, atlas_dir, icc_type = ‘icc_3’):

REQUIRED: multisession_list = 1 sessions/runs of 3D Nifti images: string (Subjects across Sessions must be in SAME order)>; atlas type = <str: ‘aal’, ‘destrieux_2009’, ‘difumo’, ‘harvard_oxford’, ‘juelich’, ‘msdl’, ‘pauli_2017’, ‘shaefer_2018’, ‘smith_2009’ or ‘talairach’>, atlas directory = <where atlas already exists or should be saved (recommend: ‘/tmp/’)>, **kwags = < additional options as required for each atlas at Nilearn datasets. Variable and value, e.g., dimension=64 can be added as instructed in the atlases documentation>
OPTIONAL: icc_type = <string (options include: ‘icc_3’,’icc_2’,’icc_1’). Default set to icc_3>

Function returns dictionary with 11 values:

• Atlas ROI Labels (‘roi_labels’): This contains the order of labels (e.g., pulled from atlas.labels)
• ICC estimates (‘est’): 1D array that contain ICCs estimated for N ROIs in atlas.
• ICC lower bound (lb) 95% CI (‘lowbound’): 1D array that contain lb ICCs estimated for N ROIs in atlas.
• ICC upper bound (up) 95% CI (‘upbound’): 1D array that contain ub ICCs estimated for N ROIs in atlas.
• Mean Squared Between Subject Variance (‘msbtwn’): 1D array that contain MSBS ICCs estimated for N ROIs in atlas.
• Mean Squared Within Subject Variance (‘mswthn’): 1D array that contain MSWS ICCs estimated for N ROIs in atlas.
• ICC estimates transformed back to space of ROI mask (‘est_3d’): Nifti 3D volume of ICC estimates
• ICC lower bound 95% CI transformed back to space of ROI mask (‘lowbound_3d’): Nifti 3D volume of lb ICC estimates
• ICC upper bound 95% CI transformed back to space of ROI mask (‘upbound_3d’): Nifti 3D volume of up ICC estimates
• Mean Squared Between Subject Variance transformed back to space of ROI mask (‘msbtwn_3d’): Nifti 3D volume of MSBS estimates
• Mean Squared Within Subject Variance transformed back to space of ROI mask (‘mswthn_ed’): Nifti 3D volume of MSWS estimates