Well, actually when we set a threshold for image analysis, in many cases, it's arbitrary. One thing you can do is to show the results (either FA values or group difference) is not overly dependent on the threshold of your choice.<br>
<br><div class="gmail_quote">On Wed, Sep 22, 2010 at 2:35 PM, Rajagopalan, Venkateswaran <span dir="ltr"><<a href="mailto:rajagov2@ccf.org">rajagov2@ccf.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Dear Dr.Mori,<br>
<br>
Thanks very much for your kind reply. Actually I don't want to delete high probability tracts as you mentioned these are the more accurate tracts I was trying to find a "acceptable" method (so that this will not be an issue when i submit an article) to threshold the tract probability values since there are lot of pixels whose probability values are close to 0 so I thought of using percentile like in outlier rejection procedure that is why i ended up choosing 5% and 95%. The threshold value you gave me (< 0.2%) looks very good. Can you give me the rationale behind choosing that number since this becomes an important question when I submit manuscripts.<br>
<br>
Thanks very much<br>
<br>
Venkat<br>
<div><div></div><div class="h5"><br>
<br>
-----Original Message-----<br>
From: <a href="mailto:mristudio-users-bounces@mristudio.org">mristudio-users-bounces@mristudio.org</a> on behalf of susumu mori<br>
Sent: Wed 9/22/2010 1:58 PM<br>
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
Subject: Re: [Mristudio-users] CST atlas<br>
<br>
Hi Venkat,<br>
<br>
I'm not sure why you want to reject >95 percentile pixels because these<br>
pixels are the best representation of the CST (highest probability). Isn't<br>
it more reasonable to use the probability threshold like >0.2?<br>
<br>
When we do FA calculation, FA of each pixel is weighted by probability. So<br>
high probability pixels have more weight. If you don't want it, you can<br>
convert the probability map to binary (1/0) by applying a threshold using<br>
RoiEditor.<br>
<br>
RoiEditor can also allows to apply a cut-off value for FA measurement. In<br>
this case, you can, for example, mask-out all pixels with probability <0.2,<br>
and then perform probability-weighted FA measurement for those pixels with<br>
>=0.2.<br>
<br>
Susumu<br>
<br>
On Wed, Sep 22, 2010 at 11:18 AM, Rajagopalan, Venkateswaran <<br>
<a href="mailto:rajagov2@ccf.org">rajagov2@ccf.org</a>> wrote:<br>
<br>
><br>
> Dear All,<br>
><br>
> I am using CST probability atlas for some calculations (i.e. measuring FA<br>
> values along CST), since the CST atlas includes probability values ranging<br>
> from 0 to 1, I want to exclude very low probability values like 0.00002 I<br>
> tried using Percentile ( since It will not raise concerns when I write an<br>
> article say I want to retain say between 5% and 95%) however since many<br>
> voxels have very low probability values this is not working good in the<br>
> sense for 95 percentile my probability value comes to 0.1745 however the<br>
> probability values range from 0.0 to 0.578 so all the higher probability<br>
> values above 0.1745 will get rejected. Any suggestions will be of great<br>
> help.<br>
><br>
> Thanks<br>
><br>
> Venkat<br>
><br>
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