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Laboratory manual ACE-IBIS Infant Study Image processing pipelines [pdf]

  • Image processing methods and pipelines
  • Guidelines for segmentation of anatomical structures
  • Geometric phantom calibration of structural MRI

Rhesus Monkey Brain Atlas: Subcortical Gray Structures [pdf] (Manual Tracing for Hippocampus, Amygdala, Caudate, and Putamen)

  • Tracing is done in a combination of the three orthogonal planes, as specified in the
    detailed methods that follow.
  • Each region of interest was originally defined in the right hemisphere. The labels
    were then reflected onto the left hemisphere and all borders checked and adjusted
    manually when necessary.
  • For the initial parcellation, the user used the “paint over function” of IRIS/SNAP on
    the T1 template of the atlas.

Regional and Lobe Parcellation Rhesus Monkey Brain Atlas [pdf] (Manual Tracing for Parcellation Template)

  • Traces are performed in a systematic order they, allowing the more easily defined
    regions to provide borders for the more difficult regions
  • Many parts of the protocol instruct the user to trace to or from the “depth” of a sulcus.
    The “depth” of a sulcus refers to the gray matter/white matter border within the
    sulcus.
  • Tracing is done in a combination of the three orthogonal planes, as specified in the
    detailed methods that follow.
  • Each region of interest was originally defined in the right hemisphere. The labels
    were then reflected onto the left hemisphere and all borders checked and adjusted
    manually when necessary.
  • For the initial parcellation, the user used the “paint over function” of IRIS/SNAP
    painting over label 1 and label 2 (GM and WM) of the hard tissue segmentation. The
    resulting labels were then dilated to fill the entire brain space.