Hi Panos when you run it with the orig you are getting voxels that happen to have an intensity of 77 and have nothing to do with lesions. Run it on the aseg
Bruce On Fri, 26 Jul 2013, Fotiadis, Panagiotis wrote: > 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 > > > _______________________________________________ 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 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
