imaging data pulled: 2019-08-29
code written: 2019-08-29
last ran: 2019-08-31
website: http://rpubs.com/navona/NM_SN_circles

This analysis compares the effect of adjusting the size of the circle diameter/radius used for reference ROI selection. Chen uses a 4mm diameter (note: our code was previously using a diameter of 5mm; this has now been changed to 4mm).


Method

Here, we review the difference between diameters of [4, 6, 8, 10], on one participant with ‘good’ data (SEN011). The two reference ROIs were consistently placed at [x=230, y=255] and [x=197, y=255], on the slice on which the SN was most visually apparent (slice 10), and then averaged. I calculated the SN NM outcome measures (signal intensity of reference region and the SN, and volume and CNR).

Data from participant SEN011, slice 10.

Data from participant SEN011, slice 10.

Summary table

diameter SI \(\mu\)\(_{REF}\) SI \(\sigma\)\(_{REF}\) SI \(\mu\)\(_{SN}\) SI \(\sigma\)\(_{SN}\) Voxels Volume CNR
4 814.85 22.84 109,222.94 8,569.42 632 252.8 6.03
6 813.31 23.06 109,289.87 8,570.74 639 255.6 6.00
8 812.27 24.24 109,252.80 8,557.91 624 249.6 5.82
10 808.37 29.10 109,043.14 8,492.95 565 226.0 5.21

Conclusion

Differences are minimal but the CNR increases as a function of diameter; we should probably maintain 4mm.

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.