Anything that is non-0 will cover the whole brain. doug Sudhin A. Shah wrote: > Hi, thank you. Is there a range in the labels that will ensure that I am > including the whole brain? I.e. I see labels for Cx, but not subcortical.. > If I take labels 1001 to 2001 ( for eg ) will that cover whole brain? > > Thank you, > S > > > > On Jun 13, 2011, at 10:59 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote: > > >> That is fine, or you can use mri_binarize with the --match option. The >> numbers that correspond to each label can be found in >> $FREESURFER_HOME/FreeSurferColorLUT.txt. You can also get at them visual as >> I described in my previous email with tkmedit: >> >> tkmedit subject orig.mgz -aux aseg.mgz -aseg >> >> doug >> >> >> Sudhin A. Shah wrote: >> >>> I mean that I am using FSL to create binary masks from freesurfer >>> parcellated regions. Unless there is a better way :) >>> >>> S >>> >>> >>> >>> On Jun 10, 2011, at 7:13 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>> wrote: >>> >>> >>> >>>> What do you mean you are doing it with FEAT? >>>> >>>> Sudhin A. Shah wrote: >>>> >>>> >>>>> Hello, >>>>> >>>>> I am a beginner so please bear with me. I want to obtain binary masks for >>>>> every region (Cortical + subcortical). I am using FSL(feat) to do this >>>>> BUT am not sure what the labels would be. >>>>> >>>>> I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz BUT >>>>> do not know which labels to use to avoid overlap and ensure full coverage. >>>>> >>>>> Thank you, >>>>> >>>>> S >>>>> >>>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> _______________________________________________ >>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> _______________________________________________ >>>> 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. >>>> >>>> >>>> >>> >>> >> -- >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> > > >
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
