Hi Derek
if you run mris_info or mris_euler_number it will tell you how many vertices/faces are in the array. I'm not sure what would cause such a high value, but you should be able to visualize it and see (once you have the vertex numbers that are in the face you can use freeview to goto them by typing the number into the "cursor" info panel at the bottom.
cheers Bruce
On Tue, 6 Oct 2015, Andrews, Derek wrote:
Dear Bruce,
Thank you for your response regarding high area values.
I have indeed observed high values (I.e. >20) in both the white and pial surfaces of my subjects, albeit only at a few vertices. The vertices indices that contain the highest values in these surface appear around ~258,000-324,000. Would you consider this the end of the array? And if not, what could cause a value of ~80 in the ~258,000 vertex of a pial surface reconstruction?
As a background to what I¹m hoping to accomplish: I am using Freesurfer features (arrays) as inputs for pattern classification, therefore I am interested in potential impact on my models due to these outliers. Smoothing reduces the effect of these outliers, however also raises the values of surrounding vertices. I am thinking of replacing these high values with an average area measure taken across all participants prior to smoothing.
Again, thank you for your insights in this topic.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate & IoPPN Student Forum Chair
Department of Forensic and Neurodevelopmental Sciences & The Sackler Institute for Translational Neurodevelopment Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 25/09/2015 17:00, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
are they only high on the pial and not on the white? I would have guessed that they would be high on both, and further that it is due to the topology correction and the quirks of the way we retesselate. One easy way to find out if this is true is if the vertex index is near the end of the list (i.e. close to the total number of vertices, since the vertices added during the correction are at the end of the array)
cheers Bruce
On Fri, 25 Sep 2015, Andrews, Derek wrote:
Dear FreeSurfer Support Team
First of all, I must thank you for your excellent software!
I have been looking at distributions of various free surfer features (histograms of the vertex wise measures). I have noticed some high values among the pial and white matter surfaces, these values range from 20-85. Again, this in only in a handful of vertices (out of millions of measures). I am wondering what could account for such a high value?
Thank you for your help in clarifying this.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
Department of Forensic and Neurodevelopmental Sciences &
The Sackler Institute for Translational Neurodevelopment Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
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