Visualization

MRview

MRview is a powerful viewer distributed with MRtrix that works well with both volume (e.g. .nii, .nii.gz) and tractography (e.g. .tck) data. It may take a while to load and navigate large tractography files.

Tips and tricks:

• Consider extracting a particular connection passing through two anatomical structures to view instead of the full tractogram. This can be done with the tractogram data, and the structures of interest:

tckedit -include structure1_roi.nii.gz -include structure2_roi.nii.gz in_tractogram.tck out_tractogram.tck

• Extracting a subset number of streamlines from tracts (e.g. 10K):

tckedit in_tractogram.tck out_tractogram.tck -number 1000

Note: MRtrix has a number of different options for manipulating tractograms which can aid the ability to visualize such tracts. Take a look through the tckedit documentation as well as both the tck2connectome and connectome2tck documentation.

ITK-SNAP

ITK-SNAP is a lightweight tool that is able to quickly open volumes and is ideal for viewing segmentation images (_dseg.nii.gz). Segmentations can be loaded as overlays and ITK-SNAP can create a 3D rendering of the contours of each label.