Hi Mo

lesion is basically anything that makes the tissue darker, so most of the things you described. For jsut a straight T1 in recon-all the algorithm is just the standard aseg. If you have a T2 or flair and maybe a PD you can use the lesion segmentation algorithms that Emily Lindemer developed and applied in a series of recent papers.

cheers
Bruce


On Mon, 20 Aug 2018, Mo Izady wrote:

        External Email - Use Caution        

Hi everyone,
I apologize for reposting this but I haven't received any response since last week. Could someone
pls help?

Here are my questions:

1) What is considered a lesion in subcortical segmentation? (tumor, MS, stroke, etc) 

2) Would you pls share the reference to the algorithm that FreeSurfer uses for segmenting lesions? 

Thanks in advance!

Mo


On Wed, Aug 15, 2018 at 4:35 PM, Mo Izady <mizadyya@asu.edu> wrote:
      Hi FreeSurfer experts,
I have two questions; any hints are greatly appreciated:

1) What is considered lesion in subcortical segmentation? (tumor, MS, stroke, etc) 

2) Would you pls share the reference to the algorithm that FreeSurfer uses for segmenting
lesions?

Thanks in advance!

Mo Izady

PhD Candidate in Neuroscience
Arizona State University

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