On qualitative assessment, the mean atrophy score in patients was 1.96 ± 0.11, significantly higher than in controls (0.65 ± 0.59, p < 0.001). Only two participants (both patients with CPEO) had focal STIR hyperintensity within EOMs, in 2/12 and 4/12 EOMs, respectively. Focal T1w hyperintensity was more common in patients than controls (72/108 muscles in patients, 49/108 muscles in controls, χ2 = 0.002). In patients this more commonly manifested as a streak (63 muscles) than a dot (nine muscles), whereas in the controls the counts were 25 and 24, respectively (Fig. 2A, 2B, 2C, 2D; Table 4). Fig. 2 MRI of the orbits in the coronal plane displaying a healthy control on the left column (panels A, C, E, G, I) and a patient with chronic progressive external ophthalmoplegia (CPEO) on the right column (panels B, D, F, H, J). Coronal T1-weighted (panels A and B) and corresponding short-tau inversion recovery (STIR, panels C and D) sequences demonstrate T1-weighted hyperintense and STIR-suppressed foci intrinsic to the extra-ocular muscles (EOMs). If the diameter of the focus was approximately equal in all dimensions in the coronal plane it was termed a 'dot’, whilst if unequal it was termed a 'streak’. An example of a ‘dot’ is demonstrated in the right inferior rectus muscle on paired panels A and C, and examples of ‘streaks’ are shown in both lateral recti on paired panels B and D respectively (arrows). Panels E and F demonstrate an example of the regions of interest (ROI) used to calculate the surface area of each of the EOMs within the right orbit in a control volunteer and CPEO patient respectively: superior-rectus levator complex (SR); superior oblique (SO); medial rectus (MR); lateral rectus (LR); and inferior rectus (IR). Central ROI were placed within the same muscles for the T2-relaxometry measurements in order to avoid contamination by the surrounding fat, as demonstrated in panels G and H within the right orbits of a control volunteer and CPEO patient respectively. Panels I and J demonstrate false colour T2-relaxometry maps Table 4 Frequency of T1-weighted magnetic resonance imaging changes in healthy control and patient extra-ocular muscles Controls Patients Muscle None Dot Streak None Dot Streak SR 16 2 0 7 0 11 IR 4 2 12 8 0 10 SO 0 14 4 4 6 8 MR 8 4 6 0 0 18 LR 13 2 3 3 2 13 IO 18 0 0 14 1 3 Total 59 24 25 36 9 63 Left and right eye combined IO inferior oblique, IR inferior rectus, LR lateral rectus, MR medial rectus, SO superior oblique, SR superior rectus