Hi Doug and Bruce, When I am running mri_binarize with aseg.mgz as input and --match 77 I get clusters, but when I run the same thing with the orig.mgz as input, I get individual voxels and not any clusters are forming. Could you please explain to me why is this happening and whether there is a way to get clusters with orig.mgz as input?
Thank you for your time. Panos ________________________________________ From: Fotiadis, Panagiotis Sent: Monday, June 10, 2013 4:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] HypoIntense Lesions Great, thank you! Panos ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 3:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions Hi Panos, I don't know an automatic way to do it. You could label it by hand on tkmedit or freeview. doug On 06/10/2013 03:31 PM, Fotiadis, Panagiotis wrote: > Hi Doug, > > Thanks for your response, it was really helpful. In addition to the previous > comments, I have some subjects that have a hematoma that is not shown in the > aseg.mgz file, and hence is not shown as a hypointense cluster after doing > the analysis provided below. Do you know if there is any other way to extract > information (such as outlining it and/or acquiring its volume) about > something like? > > Thanks again, > Panos > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, June 10, 2013 12:18 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] HypoIntense Lesions > > 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 >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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