code written: 2019-09-30
last ran: 2019-12-04
website: http://rpubs.com/navona/NM_LC_methods
github: https://github.com/navonacalarco/CurAge/blob/master/scripts/analysis/00_NM_ROI_LC_methods.Rmd

Methods

Acquistion. All data were acquired on the Siemen’s 3T Prisma at ToNI, with 15 contiguous slices and 4 measurements at a voxel size of.4x.4x.3mm\(^3\).

Processing. Images from the 4 measurements were registered to the first image using a linear transform and averaged (FSL). The data was smoothed in MATLAB.

Segmention of the LC. I recorded all slices that I judged to display a visible hyperintensity in the anatomic region of the LC. Segmentation of NM images was performed in MATLAB, mostly in keeping with the methods delineated in the Chen paper. Code can be found in 00_NM_ROI_LC.m. Our process was:

  1. A reference ROI (circle with diameter of 30mm) was manually placed in the pons (blue circle) [FIGURE A]. Signal intensity in the reference ROI was verified as approximately normally distributed.

  2. A reference landmark was manually placed at the apex of the 4th ventricle (red circle) [FIGURE B].

  3. Two ‘purported’ regions for the LC were automatically drawn on the basis of the reference landmark (yellow circles) [FIGURE C], with a diameter of 12mm, centered 6mm left/right and 5mm posterior (note: these values differ slightly from Chen; need to figure out if I’m not really in mm space). Voxels in these regions with a signal hyperintensity I > 4\(\sigma\)\(_{REF}\) were considered to be plausibly part of the LC.

Example images from SEN002, slice 6, 29 voxels found in LC

Example images from SEN002, slice 6, 29 voxels found in LC

Citation

Chen, Huddleston, Langley, Ahn, Barnum, Factor, Levey, & Hu. (2014). Simultaneous imaging of locus coeruleus and substantia nigra with a quantitative neuromelanin MRI approach. Magnetic Resonance Imaging, 32, 1301-1306.