You can merge different labels into one big label with mri_mergelabels. If you want an annotation with those labels, you can use mris_label2annot to recombine your favorites back into a annotation. doug

Simmons, Andy wrote:

Dear Doug,

Thanks very much for this - that worked perfectly for one region.

How would I display a series of labels simultaneously, for example superiorfrontal, superiorparietal and superiortemporal ?

Best wishes,

Andy

-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: 08 November 2011 18:52 To: Simmons, Andy Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visualization of FreeSurfer-defined ROI

You can run mri_annotation2label to break the annotation up into smaller labels, then display a single label in tksurfer (you can load it from the GUI or on the cmd line with -label). doug

Simmons, Andy wrote:

...

Dear Doug,

What would the equivalent process for a surface rather than a volume ?

Best wishes,

Andy SImmons

Date: Fri, 04 Nov 2011 17:30:47 -0400

From: Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] Visulaization of FreeSurfer-defined ROI

To: Jade <jadeinny8@gmail.com mailto:jadeinny8@gmail.com>

Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu

Message-ID: <4EB45987.2040001@nmr.mgh.harvard.edu mailto:4EB45987.2040001@nmr.mgh.harvard.edu>

Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Try running mri_binarize with the --match option. The match value should be the id number for your ROI as defined in $FREESURFER_HOME/FreeSurferColorLUT.txt (eg, left hippo is 17). You can then load this as a segmentation or as an overlay in tkmedit.

doug

Jade wrote:

...

Hello Freesurfer experts,

I am a beginner in using Freesurfer.

I want to make a figure illustrates a specific area of ROIs (e.g.,

lh. hippocampus). How can I visulaize the Freesurfer definded ROIs?

Thanks in advance!

---

Dr Andy Simmons

Reader in Neuroimaging & Consultant Clinical Scientist

Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre

Institute of Psychiatry, Box P089

Kings College London

De Crespigny Park

London, SE5 8AF, UK

Email - andy.simmons@kcl.ac.uk

Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338

Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institut e-of-psychiatry/

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Fax +44 (0)203 228 2116

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