Computational protocol: Parcellation of the human substantia nigra based on anatomical connectivity to the striatum☆

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Protocol publication

[…] All tractography was performed in each individual's native space. Tractography analysis was carried out from all voxels in each subject's anatomically-defined SN/VTA ROI, separately for right and left. The anatomical delineation is outlined later in the methods. To avoid erroneous tractography results, we created individual subject exclusion masks using ITK-SNAP (). The ventricles and CSF spaces were automatically defined using the “snake” function, and particular attention was paid to manually refine the region surrounding the cerebral peduncle and medial wall of the temporal lobe. Tractography was run using FSL's probtrackX software (). Each voxel was sampled 5000 times with a burn in of 1000, curvature threshold of 0.2, modelling two fibres per voxel, utilising the previously calculated warp fields. [...] The medial and lateral boundaries of the SN/VTA were defined on each subjects' MT-weighted image where it is easily distinguishable from the surrounding tissues due to its bright grey colour in contrast to the adjacent cerebral peduncle. This region was manually defined by R.C. on every visible slice (between seven to ten slices) as per ) using MRIcro (). Ten randomly selected SN/VTA ROIs were segmented by a second trained individual (C.L.) and showed high inter-rater reliability, (Intraclass correlation coefficient = 0.87, p < 0.0005, 95% confidence interval 0.129–0.973; calculated using a two-way random absolute agreement model in SPSS). A shows a single-slice single-subject example of the right SN/VTA seed. [...] To define the ventral striatum (nucleus accumbens) in our older cohort of subjects, we made a subject-derived mask for this region. We used Freesurfer's (version 4.5.0, http://surfer.nmr.mgh.harvard.edu/) automated recon-all pipeline to parcellate cortical and subcortical regions (). Each subjects' ventral striatum mask was visually inspected to ensure accurate segmentation. Subjects were excluded due to preprocessing errors (n = 4) or inaccurate segmentation after visual inspection (n = 3). For the remaining 23 participants, their ventral striatum masks were warped to MNI space using DARTEL in SPM8 () and then group-averaged and binarised. This average mask was then normalised to each individuals' native space (n = 30) using the inverse of the normalisation parameters. The aim of this approach was to obtain a target ventral striatum mask that was accurate and representative of our older cohort but the same size for each individual, hence we averaged the mask across the group. Thus we report DTI data for all 30 participants.The dorsal striatum was defined using the caudate and putamen masks from the AAL toolbox (). The group-averaged ventral striatum mask was subtracted from this caudate-putamen mask to make a non-overlapping dorsal striatum mask. This MNI-space mask was then normalised to each individuals' native space using the inverse of the normalisation parameters. A shows a single-slice single-subject subject example of the right ventral and dorsal striatum target masks. […]

Pipeline specifications

Software tools ITK-SNAP, Probtrackx, MRIcro, FreeSurfer, SPM, AAL
Applications Magnetic resonance imaging, Diffusion magnetic resonance imaging analysis
Organisms Homo sapiens
Diseases Parkinson Disease