You are guaranteed not to have overlap regardless of what you do as
there is only one label at each voxel. For Cortex, what you have is
fine. For subcortical, you can use what is in
$FREESURFER_HOME/ASegStatsLUT.txt. This has {Left,Right}-Cerebral-Cortex
which can be ignored.
doug
Sudhin A. Shah wrote:
> 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
>>> >>>>>
>>> >>>>>
>>> >>>>>
>>> ------------------------------------------------------------------------
>>> >>>>>
>>> >>>>> _______________________________________________
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>>> >>>>>
>>> >>>>>
>>> >>>> --
>>> >>>> Douglas N. Greve, Ph.D.
>>> >>>> MGH-NMR Center
>>> >>>> gr...@nmr.mgh.harvard.edu
>>> >>>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>> >>>>
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>>> >>>>
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>>> >>>>
>>> >>>
>>> >>>
>>> >> --
>>> >> 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
>>>
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>>
>
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--
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
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