Re: [Freesurfer] re Annotation2label

Hi Linn, just leave it as white. The label is just a list of vertices. doug

On 08/07/2013 05:38 AM, Linn Mittlestein wrote:

Thank you. I also have one question; it says default is "white" surface, but I want measure cortical thickness. Can I leave white in or do I change --surf to gray for this?

Kind Wishes,

Linn

On Tue, Aug 6, 2013 at 6:50 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Use --annotation aparc.a2009s
Run it with --help to see all the options.
doug


On 08/06/2013 08:24 AM, Linn Mittlestein wrote:
> Hi all,
>
> I bit confused about how to create labels from annotation2label
> command to create DLPFC. I want make DLPFC label by merging
> G_frontal_middle.label, S_frontal_inferior.label and
> S_frontal_middle.label (available in the 2009 atlas). But I only can
> get annotation2label to work with the other atlas; eg using this
command:
>
> mri_annotation2label  --subject $subject --hemi rh --outdir
> ./$subject/label
>
> But I would like 2009 atlas so for example
>
> mri_annotation2label --a2009s --subject $subject --hemi rh --outdir
> ./subject/label
>
> But this flag doesnt seem to work. Any other suggestions to get the
> label files (so i can then do mri_mergelabels and Mris_anatomical
> stats would be very appreciated, I dont think I need use tksurfer, I
> think mri_annotation2label should work somehow?
>
> Kind Wishes,
>
> Linn
>
>
> /
>
> /
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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