<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:SmartTagType
namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PostalCode"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="State"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="Street"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PlaceType"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PlaceName"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="address"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="City"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="place"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
#wmMessage v\:* {behavior:url(#default#VML);}
#wmMessage o\:* {behavior:url(#default#VML);}
#wmMessage w\:* {behavior:url(#default#VML);}
#WMMESSAGE .SHAPE
{behavior:url(#default#VML);}
#wmMessage st1\:* {behavior:url(#default#ieooui) }
/* Font Definitions */
@font-face
{font-family:"MS Mincho";
panose-1:2 2 6 9 4 2 5 8 3 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"\@MS Mincho";
panose-1:2 2 6 9 4 2 5 8 3 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
span.EmailStyle18
{mso-style-type:personal;
font-family:Arial;
color:navy;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
{page:Section1;}
/* List Definitions */
@list l0
{mso-list-id:864825958;
mso-list-type:hybrid;
mso-list-template-ids:284171266 67698705 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l0:level1
{mso-level-text:"%1\)";
mso-level-tab-stop:.5in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level2
{mso-level-tab-stop:1.0in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level3
{mso-level-tab-stop:1.5in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level4
{mso-level-tab-stop:2.0in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level5
{mso-level-tab-stop:2.5in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level6
{mso-level-tab-stop:3.0in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level7
{mso-level-tab-stop:3.5in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level8
{mso-level-tab-stop:4.0in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level9
{mso-level-tab-stop:4.5in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1
{mso-list-id:1679693955;
mso-list-type:hybrid;
mso-list-template-ids:212476134 67698705 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l1:level1
{mso-level-text:"%1\)";
mso-level-tab-stop:.5in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level2
{mso-level-tab-stop:1.0in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level3
{mso-level-tab-stop:1.5in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level4
{mso-level-tab-stop:2.0in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level5
{mso-level-tab-stop:2.5in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level6
{mso-level-tab-stop:3.0in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level7
{mso-level-tab-stop:3.5in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level8
{mso-level-tab-stop:4.0in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level9
{mso-level-tab-stop:4.5in;
mso-level-number-position:left;
text-indent:-.25in;}
ol
{margin-bottom:0in;}
ul
{margin-bottom:0in;}
-->
</style>
</head>
<body lang=EN-US link="#000000" vlink="#000000">
<div class=Section1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>We are thinking about having another
workshop in <st1:City w:st="on"><st1:place w:st="on">Hopkins</st1:place></st1:City>.
Hopefully sometime in August. We’ll send everyone a notice once the date if
fixed.<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>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<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>sjacobson@spokaneadvancedimaging.com<br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, July 08, 2008 12:28
AM<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]
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>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>How can I get information on upcoming workshops for MRI studio?<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Susan Jacobson<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><st1:City w:st="on"><st1:place w:st="on"><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Spokane</span></font></st1:place></st1:City>
Advanced Imaging Institute<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><st1:Street w:st="on"><st1:address w:st="on"><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>910 W. 5th Ave., Ste.
150</span></font></st1:address></st1:Street><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><st1:place w:st="on"><st1:City w:st="on"><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Spokane</span></font></st1:City>,
<st1:State w:st="on">Washington</st1:State> <st1:PostalCode w:st="on">99204</st1:PostalCode></st1:place><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>1-509-363-6502<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>1-509-863-3813 cell<br>
<br>
<br>
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>-------- Original Message --------<br>
Subject: Re: [Mristudio-users] Results using analyze format in<br>
DTIStudio<br>
From: susumu <<a href="mailto:susumu@mri.jhu">susumu@mri.jhu</a>.edu><br>
Date: Mon, July 07, 2008 6:24 pm<br>
To: "'DTI Studio, ROI Editor, Landmarker<br>
Questions/Support'"<mristudio-users@mristudio.org><br>
<br>
<br>
<o:p></o:p></span></font></p>
<u1:SmartTagType name="PlaceName" namespaceuri="urn:schemas-microsoft-com:office:smarttags"></u1:SmartTagType><u1:SmartTagType name="PlaceType" namespaceuri="urn:schemas-microsoft-com:office:smarttags"></u1:SmartTagType><u1:SmartTagType name="City" namespaceuri="urn:schemas-microsoft-com:office:smarttags"></u1:SmartTagType><u1:SmartTagType name="place" namespaceuri="urn:schemas-microsoft-com:office:smarttags"></u1:SmartTagType>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Graeme,</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<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.</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<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. </span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<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. </span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<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;</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
margin-left:.5in;text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'><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</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
margin-left:.5in;text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'><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</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>
</div>
<div>
<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 </span></font><o:p></o:p></p>
</div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'><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?</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'><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?</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>
</div>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabIndex=-1>
</span></font></div>
<div>
<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'> <a
href="mailto:mristudio-users-bounces@mristudio.org"><u><font color=blue><span
style='color:blue'>mristudio-users-bounces@mristudio.org</span></font></u></a> [<a
href="mailto:mristudio-users-bounces@mristudio.org" target="_blank"
mce_href="mailto:mristudio-users-bounces@mristudio.org"></a><a
href="mailto:mristudio-users-bounces@mristudio.org"><u><font color=blue><span
style='color:blue'>mailto:mristudio-users-bounces@mristudio.org</span></font></u></a>]
<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> <a
href="mailto:Mristudio-users@mristudio.org"><u><font color=blue><span
style='color:blue'>Mristudio-users@mristudio.org</span></font></u></a><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>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hello,<br>
<br>
At the <st1:City u2:st="on"><st1:place u2:st="on"><st1:City w:st="on"><st1:place
w:st="on">Toronto</st1:place></st1:City></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 u2:st="on"><st1:PlaceType u2:st="on"><st1:place w:st="on"><st1:PlaceType
w:st="on">University</st1:PlaceType></st1:PlaceType> of <st1:PlaceName u2:st="on"><st1:PlaceName
w:st="on">Toronto</st1:PlaceName></st1:place></st1:PlaceName></st1:place><br>
<a href="mailto:graeme.schwindt@gmail.com" target="_blank"
mce_href="mailto:graeme.schwindt@gmail.com"></a><a
href="mailto:graeme.schwindt@gmail.com"><u><font color=blue><span
style='color:blue'>graeme.schwindt@gmail.com</span></font></u></a><br>
416.546.5453 <o:p></o:p></span></font></p>
</div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center>
</span></font></div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>_______________________________________________<br>
Mristudio-users mailing list<br>
<a href="http://email.secureserver.net/pcompose.php#Compose"
mce_href="http://email.secureserver.net/pcompose.php#Compose"><u><font
color=blue><span style='color:blue'>Mristudio-users@mristudio.org</span></font></u></a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/mristudio-users"
target="_blank"
mce_href="http://lists.mristudio.org/mailman/listinfo/mristudio-users"></a><a
href="http://lists.mristudio.org/mailman/listinfo/mristudio-users"><u><font
color=blue><span style='color:blue'>http://lists.mristudio.org/mailman/listinfo/mristudio-users</span></font></u></a><o:p></o:p></span></font></p>
</div>
</div>
</body>
</html>