Hi, Is there anyway to know all the label #s that are in aparc+aseg-inhighres.mgz.
Thank you, S On 06/13/11, "Sudhin A. Shah" <sut2...@med.cornell.edu> wrote: > > > Hi Sorry for bothering you again, but I am not sure I understand. > > I was running whole brain correlation analysis (voxel by voxel). BUT for > comparison purposes, I want to compute region by region correlation matrix. > So, I want to divide up the brain into freesurfer parcellated regions - i.e. > with no overlap, but with full coverage of whole brain. > > I have looked at FreeSurferColorLUT.txt and am confused because there are > several sets and overlap (eg. 19 and 55 vs 2035..) > > If I use the following, can I ensure no overlap and full coverage? > 1)Subcortical: 9-13, 16-19, 48-55, 58 - 59, 85,86 > 2)Cortex: 1002- 1034, 2002- 2034 > > I am asking if there is an established list of whole brain parcellations > before I rely on label names to choose the ROIS > > On 06/13/11, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > > 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 > > >>>>> (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 > > >>>> (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 > > >>>> (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 > > (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) > > > >
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