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 <greve@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 <greve@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 <greve@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
>>>> greve@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
>> greve@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
greve@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