it sounds like you want a different parcellation of the lateral prefrontal cortex than what is offered by the default atlas (aparc, AKA the desikan atlas) - I suggest you load in ?h.aparc.a2009s.annot (aka the destrieux atlas) as your annotation in tksurfer and select the annotations of the PFC that you want from there and save as labels. The aparc.a2009 annotation offers a more fine grained parcellation of the PFC - e.g. you can get the DLPFC by merging the middle frontal gyrus & middle frontal sulcus parcellations.


On Mon, Mar 25, 2013 at 3:19 AM, Anupa AV <av.anupa@yahoo.com> wrote:
Dear Laura,
Thank you so much.
It worked well.
Do you know how to make cuts on the merged label, for eg. if I need to seperate DLPFC from premotor cortex.


From: Laura M. Tully <tully.laura@googlemail.com>
To: Anupa AV <av.anupa@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Sunday, March 24, 2013 12:20 AM
Subject: Re: [Freesurfer] Merging PArcellation labels

First save each parcellation that you want as its own separate label by selecting it in tksurfer (simply click on it with  your mouse and its boarder will be highlighted in yellow) and then file -> label -> save selected label...  Then you can merge these separate labels into one label at the command line using mri_mergelabels -i [labelfile1] -i [labelfile2] -o [newlabelfile.label]

If doing glms from the command line you can then feed mri_glmfit the label with the --label option. This will conduct the glm in the region specified in the label only (i.e. an roi analysis) 

There is also a quick way to turn all of the desikan parcellations into individual label files at the command line using mri_annotation2label I think, but I can't remember precisely. This is a lot faster than using tksurfer as it simply dumps all the individual parcellations into a specified output directory. But I don't know if you can do it with the Destrieux atlas parcellations (if you were interested in doing that.) 

Laura. 





On Sat, Mar 23, 2013 at 2:36 AM, Anupa AV <av.anupa@yahoo.com> wrote:
Dear All,

Can anyone tell me how to merge the parcellation labels using tksurfer.? For eg. How can I merge, Superior frontal gyrus, middle frontal gyrus and caudal middle frontal gyrus.

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--
--
Laura M. Tully, MA
Social Neuroscience & Psychopathology, Harvard University
Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience
ltully@mednet.ucla.edu 
ltully@fas.harvard.edu
310-267-0170
--
My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura

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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.





--
--
Laura M. Tully, MA
Social Neuroscience & Psychopathology, Harvard University
Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience
ltully@mednet.ucla.edu 
ltully@fas.harvard.edu
310-267-0170
--
My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura