Re: [Freesurfer] high area.pial values

[Andrews, Derek]

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.andr...@kcl.ac.uk





On 25/09/2015 17:00, "Bruce Fischl"  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.andr...@kcl.ac.uk
>> 
>> 
>> 
>>___
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>is
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>contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] high area.pial values

[Bruce Fischl]

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.andr...@kcl.ac.uk





On 25/09/2015 17:00, "Bruce Fischl"  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.andr...@kcl.ac.uk



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[Freesurfer] high area.pial values

[Andrews, Derek]

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.andr...@kcl.ac.uk

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

Re: [Freesurfer] high area.pial values

[Bruce Fischl]

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.andr...@kcl.ac.uk 



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