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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 Graeme,<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'>I believe FA, ADC, and color maps are
insensitive to right-left, front-back, and up-down flip. It becomes in issue
when you do fiber tracking.<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'>DtiStudio support the Analyze format to
save 3D images after tensor calculation. If you save data as Analyze and read
as Analyze, the orientation should be correct, but if it is saved as Analyze
and read as Raw, you’d find that the axial image is upside-down, due to
Neurology – Radiology conventions. <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'>In DtiStudio, we do not support tensor
calculation of DWIs in the Analyze format. Also, it is difficult to confirm
what would happen if DtiStudio processes data partially processed by other
software programs because it is difficult for us to test many combinations of data
processing by multiple programs. I would suggest to stick to single software
for DWI – tensor calculation. <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'>It is indeed interesting that you saw 0.2
FA difference by going through the Analyze format, but again, it difficult for
us to follow the results that were not processed by DtiStudio for the entire
processing. If you experience 0.2 difference with and without AIR in DtiStudio,
we would definitely look into the issue. If you mean difference is between;<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 style='margin-left:.5in;text-indent:-.25in;mso-list:l1 level1 lfo1'><![if !supportLists]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><span style='mso-list:Ignore'>1)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>raw DWI -> DtiStudio -> AIR in DtiStudio -> FA<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l1 level1 lfo1'><![if !supportLists]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><span style='mso-list:Ignore'>2)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>raw DWI -> FSL (eddy correction) -> Analyze -> DtiStudio
-> FA<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'>We first need to know <o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><span style='mso-list:Ignore'>1)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>how did you read Analyze into DtiStudio?<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><span style='mso-list:Ignore'>2)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Have you compared raw DWIs and Analyze (after FSL eddy correction)
DWIs?<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>
<div>
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face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
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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>Graeme Schwindt<br>
<b><span style='font-weight:bold'>Sent:</span></b> Sunday, July 06, 2008 2:44
PM<br>
<b><span style='font-weight:bold'>To:</span></b> Mristudio-users@mristudio.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [Mristudio-users] Results
using analyze format in DTIStudio</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>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hello,<br>
<br>
At the <st1:City w:st="on"><st1:place w:st="on">Toronto</st1:place></st1:City>
workshop, it was mentioned that loading analyze format images into dtistudio is
not recommended as the images are loaded in flipped, and so the gradient tables
will not apply properly, as I understood. <br>
<br>
We have analyzed a couple of subjects from two separate datasets using both the
raw dicoms in dtistudio (following AIR), but also with some analyze format
images that have been preprocessed in FSL (eddy-current correction). <br>
<br>
Surprisingly, the FA maps and colour maps are qualitatively very similar
between the two methods, which is counterintuitive given the improper mapping
between the gradient table and orientation of the analyze imgs. Also, the FA
values are generally <i><span style='font-style:italic'>higher</span></i> by
0.2 or so in the analyze version of the analysis. Is it possible that the
analyze format is actually being read properly though its display is wrong? Any
thoughts on the validity of using analyze format would be appreciated.<br>
<br>
Thanks,<br>
Graeme<br>
<br>
<br clear=all>
<br>
-- <br>
Graeme C. Schwindt, HBSc<br>
MD/PhD Student<br>
<st1:place w:st="on"><st1:PlaceType w:st="on">University</st1:PlaceType> of <st1:PlaceName
w:st="on">Toronto</st1:PlaceName></st1:place><br>
<a href="mailto:graeme.schwindt@gmail.com">graeme.schwindt@gmail.com</a><br>
416.546.5453 <o:p></o:p></span></font></p>
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