pipeline for PREprocessing and Extraction of the MACaque brain Surface
PREEMACS is a set of tools taken from several image processing softwares commonly used for human data analysis, customized for Rhesus monkeys brain surface extraction and cortical thickness analysis.
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Performs volume orientation, image cropping, intensity non-uniformity correction, and volume averaging, ending with skull-stripping (PREEMASK brainmask tool) through a convolutional neural network.
Performs a quality control using an adaptation of MRIqc method to extract quality metrics that are then used to determine the likelihood of accurate brain surface estimation.
This module estimates the white matter and pial surfaces from the T1-weighted volume (T1w) using an NHP customized version of FreeSurfer v6.
In order to customized FreeSurfer to NHP, based on 33 subjects, 29 from PRIME-DE (Milham et al., 2018) and 4 from UNAM-INB data sets, PREEMACS has developed.
- PREEMACS FreeSurfer segmentation atlas, with cortical and subcortical labels
- PREEMACS Rhesus parameterization template that includes the Rhesus curvature and sulcal pattern templates for individual monkey WM surface registration
- PREEMACS Rhesus average surface for final mapping of vertices across all animals
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- Singularity Container