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) > -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514
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