cluster/peak vertex infomation

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Catherine Alexandra Hartley

14 Sep 2007 14 Sep '07

10:52 a.m.

Hi,

I have a few questions, the answers to which probably all involve running mri_surfcluster with the correct arguments specified.

1) What is the easiest way to obtain peak vertex information from a given cluster?

2) For a given sig.mgh file, is there a command which outputs a list/text file of all clusters present?

3) Is there a way to restrict the clusters displayed in the sig.mgh file to clusters of a given # of vertices or larger?

Thanks in advance for your help!

-Cate

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Robert Levy

14 Sep 14 Sep

2:25 p.m.

...

What is the easiest way to obtain peak vertex information from a given cluster?

For a given sig.mgh file, is there a command which outputs a list/text file of all clusters present?

Hi,

The --sum option allows you to provide a name for the textfile it will generate containing information about each cluster. In the text file, each row will have a MaxVert field.

mri_surfcluster ... --src <inputfile>.mgh --sum <sumfilename>.sum

...

Is there a way to restrict the clusters displayed in the sig.mgh file to clusters of a given # of vertices or larger?

--minarea area "Minimum surface area (in mm^2) that a set of contiguous vertices must achieve in order to be considered a cluster." https://surfer.nmr.mgh.harvard.edu/fswiki/mri_5fsurfcluster

-- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: levy@nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

Doug Greve

16 Sep 16 Sep

4:41 p.m.

Yep, all these things are done as part of mri_surfcluster. Have you looked at the --help?

doug

On Fri, 14 Sep 2007, Catherine Alexandra Hartley wrote:

...

Hi,

I have a few questions, the answers to which probably all involve running mri_surfcluster with the correct arguments specified.

What is the easiest way to obtain peak vertex information from a given cluster?

For a given sig.mgh file, is there a command which outputs a list/text file of all clusters present?

Is there a way to restrict the clusters displayed in the sig.mgh file to clusters of a given # of vertices or larger?

Thanks in advance for your help!

-Cate _______________________________________________ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Catherine Alexandra Hartley
Doug Greve
Robert Levy