<br><div class="gmail_quote">Thank you very much Mr. Susumu,<br><br>with ROI editor I can extract the pixel values in a txt file, that is what I want, thank you. <br><br>But I have a problem. The FA mean value that results in DTI Studio is different that the FA mean value that results in ROI editor, with the same binary image, why occur this?. <br>
<br>For example, with the same mask of the genu of corpus callosum, I have the same number of pixels (2835 pixels) but the FA statistics is different. <br><br>DTI studio: <br> FA<br> Max. of ImgVal: 0.9690<br>
Min. of ImgVal: 0.0591<br> <b> Mean of ImgVal: 0.5385</b><br> Std. of ImgVal: 0.1689 <br><br>ROI editor:<br> Min: 0.06<br> Max: 0.97<br> <b>Mean: 0.45</b><br> Std: 0.17<br>
<br><br><br>Could you explain me why the FA mean values are different? <br>THANK YOU<br><br>Javier<br><br><div class="gmail_quote">2009/3/14 susumu <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>></span><div>
<div></div><div class="h5"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div link="blue" vlink="blue" lang="EN-US">
<div>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Hi Javier,</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">I'm not sure if I'm answering your
question, but here I listed what you can do after you get a tractgraphy result;</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">1) Click the "statistics" button
and specify an MRI image (e.g. FA map) you want to quantify. This gives you the
average and standard deviation of all pixels included in the tract (this is not
what you want).</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">2) Then click "profile" button.
This give you pixel values within each slice in axial, coronal, and sagittal
orientations. This works nicely if the tract of your interest has a linear shape.
For tracts like the corpus callosum (U-shape), this approach has some issue.</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">3) Save the tract as a binary image (1/0
map). Load this binary image as an image to RoiEditor as well as a map you want
to quantify (e.g. FA map). Using the binary image and the thresholding tool, define
an object that identify pixels with value "1"; namely, redefine the
tract as an object. Bring the FA map as an active image and right-click the
object you defined in the "object list". This allows export (text
file) of FA values of all pixels that belong to the tract you defined. You can
read this text file into Excel and create a histogram</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">4) You can normalize the binary image to
one of the atlas provided in Landmarker. By normalize population data, you can
create probabilistic tract maps. Using RoiEditor, you can mask FA maps by
tractography results and then normalize. This may allow you to do pixel-based
analysis in an atlas space. After normalization, you can also
"segment" the tracking result into the corpus callosum region and
corona radiata region by combining your binary tracking image and "white
matter parcellation map (WMPM)" provided in RoiEditor.</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">I must admit that currently manuals of RoiEditor
and Landmarker are very limited. We are working on it and it may take some
time. If you think one of the above 4 methods can provide what you want, you
can contact us for more specific instruction.</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Susumu</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<div>
<div style="text-align: center;" align="center"><font size="3" face="Times New Roman"><span style="font-size: 12pt;">
<hr align="center" size="2" width="100%">
</span></font></div>
<p><b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma; font-weight: bold;">From:</span></font></b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma;"> <a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>
[mailto:<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>] <b><span style="font-weight: bold;">On Behalf Of </span></b>Javier Navas<br>
<b><span style="font-weight: bold;">Sent:</span></b> Thursday, March 12, 2009
8:33 PM<br>
<b><span style="font-weight: bold;">To:</span></b> DTI Studio, ROI Editor,
Landmarker Questions/Support<br>
<b><span style="font-weight: bold;">Subject:</span></b> Re: [Mristudio-users]
Extract values of the Fiber tract ROI</span></font></p>
</div><div><div></div><div>
<p><font size="3" face="Times New Roman"><span style="font-size: 12pt;"> </span></font></p>
<p style="margin-bottom: 12pt;"><font size="3" face="Times New Roman"><span style="font-size: 12pt;">Hi Susumu,<br>
<br>
I`m talking about the statistics of the fiber tracking results as an ROI. I
want to extract all the voxels values in the FA map that are included in the
corpus callusum tract to a text file. I don`t want only the mean or the
max/minimum value. Becouse I want to do a parcellation of the corpus callosum
and do a correlation of this values with the age or the IQ of the pacients.<br>
<br>
I´m working with the software some months ago, and I`m new in the list. This is
my first message. Thank you for your answer.<br>
<br>
</span></font></p>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size: 12pt;">2009/3/13 susumu <<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>></span></font></p>
<div link="blue" vlink="purple">
<div>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Hi Javier,</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Are you talking about the statistics of the ROI you drew or
using the fiber tracking results as an ROI?</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Susumu</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: "Courier New";">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span></font></p>
<p><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: "Courier New";">To unsubscribe this mailing list, please go to <a href="http://www.mristudio.org" target="_blank">www.mristudio.org</a> / Mailing
List / Mristudio-users. There you can find the unsubscribe option.</span></font></p>
<p><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: "Courier New";">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<div>
<div style="text-align: center;" align="center"><font size="3" face="Times New Roman"><span style="font-size: 12pt;">
<hr align="center" size="2" width="100%">
</span></font></div>
<p><b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma; font-weight: bold;">From:</span></font></b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma;"> <a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>
[mailto:<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>]
<b><span style="font-weight: bold;">On Behalf Of </span></b>Javier Navas<br>
<b><span style="font-weight: bold;">Sent:</span></b> Wednesday, March 11, 2009
8:15 AM<br>
<b><span style="font-weight: bold;">To:</span></b> <a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><br>
<b><span style="font-weight: bold;">Subject:</span></b> [Mristudio-users] Extract
values of the Fiber tract ROI</span></font></p>
</div>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size: 12pt;"> </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size: 12pt;">Dear all,<br>
<br>
I`m working in Fiber Tracking of the corpus callosum with DTIstudio,<br>
<br>
I want to extract the values of my ROI (the statistics with the number of
fibers selected, length of fibers, FA values...) to a text file or SPSS
archive, but I don`t know how can I do it.<br>
<br>
<br>
Thank you for help me,<br>
<br>
Javier </span></font></p>
</div>
</div>
</div>
</div>
<p style="margin-bottom: 12pt;"><font size="3" face="Times New Roman"><span style="font-size: 12pt;"><br>
_______________________________________________<br>
Mristudio-users mailing list<br>
<a href="mailto:Mristudio-users@mristudio.org" target="_blank">Mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/mristudio-users" target="_blank">http://lists.mristudio.org/mailman/listinfo/mristudio-users</a></span></font></p>
</div>
<p><font size="3" face="Times New Roman"><span style="font-size: 12pt;"> </span></font></p>
</div></div></div>
</div>
<br>_______________________________________________<br>
Mristudio-users mailing list<br>
<a href="mailto:Mristudio-users@mristudio.org" target="_blank">Mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/mristudio-users" target="_blank">http://lists.mristudio.org/mailman/listinfo/mristudio-users</a><br>
<br></blockquote></div></div></div><br>
</div><br>