Structural

Freesurfer

The FreeSurfer programme was developed to enable cortical surface reconstructions based on MR image data. The programme itself is available freely for download for all platforms, however both the BCNI and WBIC systems already have it installed.

This PDF [[1]] is a quick guide to FreeSurfer for novices. It begins with a recap of how set up a VNC server/viewer and some basic linux commands before diving in to Freesurfer itself and explains how to check the reconstructions for errors in segmentation that may impact on the accuracy of the surfaces.

You should make sure to check out the FreeSurfer wiki and in particular their tutorials.

Some of the key publications are [please edit as required!]:

• Desikan, R. S., Ségonne, F., Fischl, B., Quinn, B. T., Dickerson, B. C., Blacker, D., … Killiany, R. J. (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. NeuroImage, 31(3), 968–80. doi:10.1016/j.neuroimage.2006.01.021 Pubmed

• Yendiki, A., Koldewyn, K., Kakunoori, S., Kanwisher, N., & Fischl, B. (2013). Spurious group differences due to head motion in a diffusion MRI study. NeuroImage, 88, 79–90. doi:10.1016/j.neuroimage.2013.11.027 Pubmed

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