The MRI data were collected using a 3.0 Tesla GE MR750 scanner (GE Healthcare, Little Chalfont, UK). Three sequences were implemented: Sagittal 3D T1 (GE BRAVO sequence, FOV 256 mm, slice thickness 1 mm, Discovery MR750, TE 2.7 ms, TR 7.2 ms, Flip angle 12°, pixel spacing 1 mm), FLAIR CUBE (GE CUBE T2 FLAIR sequence, FOV 240 mm, slice thickness 1.2 mm, acquisition matrix (frequency × phase) 256 × 244, TE 163 ms, TR 8000 ms, Flip angle 90°, pixel spacing 0.47 mm), and DTI pulse sequence (spin echo, 64 directions, FOV 256 mm, acquisition matrix (frequency × phase) 128 ×128, slice thickness 2 mm, TE 83 ms, TR 8325 ms).
Probabilistic tractography, as described by Sherbondy et al.,
19 was used to reconstruct OT and OR fibers. The DTI and FLAIR T2 images were coregistered to high resolution T1 structural image. Prior to the reconstruction of the OT and OR, three regions of interest (ROI) were determined. For OT identification the first ROI (diameter, 10 mm) was placed at the chiasm and deterministic tractography was used to follow the optic tract fibers from the chiasm to the LGN, where a second ROI (7 mm) was placed. For OR reconstruction, a third ROI covering the calcarine sulcus was drawn manually in each hemisphere. Probabilistic tractography software (ConTrack is a part of mrDiffusion package available for download at
http://sirl.stanford.edu/software/, in the public domain) was run between the first (chiasm) ROI and the second (LGN) ROI to reconstruct the OT. Five thousand fibers were collected initially and a scoring algorithm was used to select the best 500 fibers. Optic tract fibers were then manually cleaned using Quench software (Quench is a part of mrDiffusion package available for download at
http://sirl.stanford.edu/software/, in the public domain). A similar process was employed to reconstruct OR, but second (LGN) and third (calcarine sulcus) ROIs were used instead. Initially, 70000 fibers were collected for OR tractography, of which 30000 best fibers were selected by scoring algorithm. Fibers were again cleaned using Quench software (
Fig. 1A).
The MS lesions were identified on coregistered FLAIR T2 and T1 images, and segmented semiautomatically using ITK-SNAP software (ITK-SNAP is a part of mrDiffusion package available for download at
http://www.itksnap.org/pmwiki/pmwiki.php, in the public domain). Lesions then were intersected with visual pathway fibers to calculate lesions volume within and outside of OR (
Fig. 1B). Averaged (between left and right sides) lesion volume was used for analysis. The DTI indices (FA, MD, AD, and RD) were calculated along OR using function of ConTrack software.