Connectome Mapper with lesioned brains

[Zoe Woodhead]

Hi there,

I'm hoping to use Connectome Mapper to produce connectivity matrices of DTI data from stroke patients. The trouble I've been having is that, in my experience, Freesurfer inflation of damaged brains is sub-optimal at best. Does anyone have any experience of using Freesurfer with damaged brains? Is there a way to tweak the recon process to get good results?

Alternatively, if I can't use Freesurfer, is there a way to import ROIs that I have manually mapped onto the (folded) cortex into Connectome Mapper, so that I can proceed from the Tractography stage and bypass the previous steps?

Any advice wold be appreciated!

Many thanks,

Zoe Woodhead