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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Christian,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>As Jun Yi said, you can get statistics at
each coronal section using the “profile” button. This may be a good
approach to study the optic radiation in the occipital lobe, although it should
include not only the OR but also other fibers such as IFO and ILF as you can
see from your reconstruction results. By adding more ROI in the LGN, the
specificity to the OR may increase but you may loose a lot of the OR
(sensitivity) as an expense of unknown increase in the specificity. The tracts
in the green area is a mixture of many tracts anyway and extract of the pure OR
may be impossible by DTI.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>The CUT operation is always a two-ROI
method, which can’t be combined with third ROI. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Susumu<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b><span style='font-weight:
bold'>On Behalf Of </span></b>Jun Yi Wang<br>
<b><span style='font-weight:bold'>Sent:</span></b> Thursday, November 06, 2008
9:40 AM<br>
<b><span style='font-weight:bold'>To:</span></b> c.bieck@t-online.de;
mristudio-users@mristudio.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users]
Optic radiations</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi Christian,<o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>After you click on the Statistics button, you can select a parameter
and click on the Statistics Profile button to open up the list of values at
each slice. For you case, you can look at the coronal section and select
the range of slices you desire. You can copy/paste your selection into a
spreadsheet.<o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Jun Yi<o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'><b><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> Christian
Bieck <c.bieck@T-Online.de><br>
<b><span style='font-weight:bold'>To:</span></b> mristudio-users@mristudio.org<br>
<b><span style='font-weight:bold'>Sent:</span></b> Thursday, November 6, 2008
3:13:00 AM<br>
<b><span style='font-weight:bold'>Subject:</span></b> [Mristudio-users] Optic
radiations<br>
</span></font><br>
<font size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>This
message seems to have bounced due to the attached picture exceeding the size
limit, so I uploaded the picture instead.</span></font><br>
<br>
<br>
<font color=black face="Courier New"><span style='font-family:"Courier New";
color:black'>Hello, </span></font><br>
<br>
<br>
<font color=black face="Courier New"><span style='font-family:"Courier New";
color:black'>Thank you very much for the very fast replies. </span></font><br>
<font color=black face="Courier New"><span style='font-family:"Courier New";
color:black'>I tried using the CUT operations in the Fiber Tab after fiber
tracking, but could not achieve any satisfactory results as the CUT operation
ended in adding fibers that were not previously there. This may be due to, as
Jun Yi Wang wrote, the CUT operation not being able to be combined with other
operations (AND, OR, NOT) of which I made heavy use during extracting the optic
radiation. </span></font><br>
<font color=black face="Courier New"><span style='font-family:"Courier New";
color:black'>Basing the application of the AND, OR and NOT operations on the
anatomy of the optic radiation as detailed in neuroanatomic publications, I
ended up with something along the lines of what you see in the attached picture
(<a
href="http://i202.photobucket.com/albums/aa215/Senalsun/Opticradiationscut.jpg"
target="_blank">http://i202.photobucket.com/albums/aa215/Senalsun/Opticradiationscut.jpg</a>).
While there is still *a lot* of fine-tuning to be done, I would like to know if
there is a way of getting rid of the part circled in red so that I may only get
the FA statistics of the optic radiation circled in green, without any of these
posterior fibers getting cut out in the process.</span></font><br>
<br>
<font color=black face="Courier New"><span style='font-family:"Courier New";
color:black'>As an alternative way, is it possible to extract the saved Fiber
ROIs and FA values as a spreadsheet so I could copy it into Excel or SPSS? My
supervisor told me it would be a good idea, if all else fails, to put the Fiber
ROI data into a spreadsheet, then only look at the coordinates beyond a certain
x, y or z value signifying the fiber tracts in the visual cortex and then look
these positions up in the FA values map. </span></font><br>
<br>
<font color=black face="Courier New"><span style='font-family:"Courier New";
color:black'>Again, thank you very much for your time and help. </span></font><br>
<br>
<br>
<font color=black face="Courier New"><span style='font-family:"Courier New";
color:black'>Sincerely, </span></font><br>
<font color=black face="Courier New"><span style='font-family:"Courier New";
color:black'>Christian Bieck</span></font><br>
<br>
<br>
<o:p></o:p></p>
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