imaging data pulled: 2019-08-27
code written: 2019-08-29
last ran: 2019-08-31
website: http://rpubs.com/navona/NM_SN_multislice

This analysis calculates the SN NM outcome measures (signal intensity of reference region and the SN, and volume and CNR) across all slices in which the SN is visually apparent, in keeping with the Chen paper.


Method

I selected participant SEN010, whose SN is visually apparent in 4/15 slices, namely slices 9-12. I had previously judged this participant’s SN to be most prominent in slice 10. The data looks as follows:

FSL greyscale; min -280, max 3000. Blur near ears to anonymize. Reference region is 5 radians at 3 SD threshold.

FSL greyscale; min -280, max 3000. Blur near ears to anonymize. Reference region is 5 radians at 3 SD threshold.

Summary table

Slice SI \(\mu\)\(_{REF}\) SI \(\sigma\)\(_{REF}\) SI \(\mu\)\(_{SN}\) SI \(\sigma\)\(_{SN}\) Voxels Volume CNR
9 741.14 22.25 108061.2 7290.99 339 135.6 4.24
10 742.01 23.85 108900.9 8834.69 621 248.4 5.38
11 760.84 18.87 108574.6 10042.92 835 334.0 5.45
12 781.70 27.87 103808.2 9346.65 211 84.4 3.64
Weighted means/sums
9-12 753.88 21.93 108087.5 9130.59 2006 802.4 5.03
Note:
Voxels and Volume variables are sums, all others are weighted averages.

Conclusion

Though signal intensity doesn’t vary widely across slice, we should measure the SN across slices to ensure accurate voxel and volume calculations.

participant_id SN_sliceRange SN_sliceCount SN_slicePrimary
SEN002 8-11 4 9
SEN003 9-11 3 10
SEN007 8-10 3 9
SEN010 9-12 4 10
SEN011 9-12 4 10
SEN012 8-10 3 9
SEN013 9-11 3 10
SEN014 9-11 3 10
SEN015 9-11 3 10
SEN018 8-9 2 9
SEN019 11-13 3 12
SEN020 9-11 3 10
SEN024 9-11 3 9
SEN026 8-10 3 9
SEN027 9-10 2 9
SEN029 8-10 3 8
SEN031 8-9 2 8

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.