On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote:
Hi Doug and Bruce,
Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 would work great as well. Do you know where I could look for them?
This is already done in recon-all (aseg.mgz and aseg.stats)
In addition, Doug besides the WM hypointensities in the aseg.stats is there something that shows the number of lesions, instead of the volume (or the volume that corresponds to each lesion)?
That is not output by default, but you can get it relatively easily in two steps: mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77 ------>> This creates a binary image Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and volume of each lesion will be in the summary file doug
Thanks for your help, Panos ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 11:52 AM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions
Hi Panos
sorry, forgot to respond to this. We have tools for labeling hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It might work on those if you also had a good T1 and some training data. Doug might know
cheers Bruce
On Mon, 10 Jun 2013, Fotiadis, Panagiotis wrote:
Hi FreeSurfer Community,
I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan.
Thank you, Panos _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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