I just want print the list of vertices with their contrast percentages into an ascii file.

Regards,

Don

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Wednesday, August 13, 2014 10:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] quick pointer: tool to extract gray/white contrast vectors from [lr]h.w-g.pct.mgh

I guess I don't understand what it is you want exactly. the gray/white contrast file is in the surf folder. Do you want to compute a mean over a given set of vertices?

On 8/13/14 10:06 AM, Krieger, Donald N. wrote:

Here is a fragment of the help text for recon-all which pointed me towards this:

WM/GM Contrast (-<no>pctsurfcon)

Computes the vertex-by-vertex percent contrast between white and gray matter.

The computation is:

         100*(W-G)

   pct = ---------

         0.5*(W+G)

The white matter is sampled 1mm below the white surface. The gray matter is

sampled 30% the thickness into the cortex. The volume that is sampled is

rawavg.mgz.  The output is stored in the surf dir of the given subject as

?h.w-g.pct.mgh.  Non-cortical regions (medial wall) are zeroed.

It is this “pct” value along with the coordinates of the vertex that I am interested in.

Regards,

Don

Don Krieger, Ph.D.

Department of Neurological Surgery

University of Pittsburgh

(412)648-9654 Office

(412)521-4431 Cell/Text

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Wednesday, August 13, 2014 10:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] quick pointer: tool to extract gray/white contrast vectors from [lr]h.w-g.pct.mgh

What do you mean by contrast vectors?

On 8/13/14 9:36 AM, Krieger, Donald N. wrote:

What is the tool to extract the contrast vectors from surf/[ lr]h.w-g.pct.mgh ?

Thanks,

Don

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