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 [fis...@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 >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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