Derivation of Brain Structure Volumes from MRI Neuroimages hosted by NDAR using LONI Workflows

LONI used de-identified data from NDAR's cloud and a LONI image processing pipeline to perform a secondary structural MRI study. The workflow used in this study pulls data from and provided by NDAR to an instance on a LONI cloud, aligns data to a standard orientation using FSLreorient2stsd, and undergoes further image processing to eventually identify, extract, and analyze cortical and sub-cortical structures in different MRI brain volumes. Two methods were used for this image processing: the first uses Freesurfer Recon_All to extract brain matter, align the data to an atlas, and identify, extract and analyze regions of interest; the second uses FSL to extract brain matter (BET), align the data to an atlas, and extract ROIs (FIRST). The second method also uses Freesurfer (mri_segstats) to perform statistical analysis of these ROIs. Lastly, the pipeline pushes the data processed and extracted by Freesurfer and FSL back to NDAR's cloud.