<html><body><div>How can I get information on upcoming workshops for MRI studio?</div>
<div> </div>
<div>Susan Jacobson</div>
<div>Spokane Advanced Imaging Institute</div>
<div>910 W. 5th Ave., Ste. 150</div>
<div>Spokane, Washington 99204</div>
<div>1-509-363-6502</div>
<div>1-509-863-3813 cell<BR><BR>
<BLOCKQUOTE style="PADDING-LEFT: 8px; MARGIN-LEFT: 8px; BORDER-LEFT: blue 2px solid" webmail="1">-------- 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>
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<div><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">Hi Graeme,</SPAN></FONT></div>
<div><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"></SPAN></FONT> </div>
<div><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">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></div>
<div><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"></SPAN></FONT> </div>
<div><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">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></div>
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<div><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">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></div>
<div><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"></SPAN></FONT> </div>
<div><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">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></div>
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<P class=MsoNormal style="MARGIN-LEFT: 0.5in; TEXT-INDENT: -0.25in; mso-list: l1 level1 lfo1"><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"><SPAN style="mso-list: Ignore">1)<FONT face="Times New Roman" size=1><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></FONT></SPAN></SPAN></FONT><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">raw DWI -> DtiStudio -> AIR in DtiStudio -> FA</SPAN></FONT></div>
<P class=MsoNormal style="MARGIN-LEFT: 0.5in; TEXT-INDENT: -0.25in; mso-list: l1 level1 lfo1"><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"><SPAN style="mso-list: Ignore">2)<FONT face="Times New Roman" size=1><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></FONT></SPAN></SPAN></FONT><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">raw DWI -> FSL (eddy correction) -> Analyze -> DtiStudio -> FA</SPAN></FONT></P>
<div><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"></SPAN></FONT> </div>
<div><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">We first need to know </SPAN></FONT></div>
<P class=MsoNormal style="MARGIN-LEFT: 0.5in; TEXT-INDENT: -0.25in; mso-list: l0 level1 lfo2"><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"><SPAN style="mso-list: Ignore">1)<FONT face="Times New Roman" size=1><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></FONT></SPAN></SPAN></FONT><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">how did you read Analyze into DtiStudio?</SPAN></FONT></P>
<P class=MsoNormal style="MARGIN-LEFT: 0.5in; TEXT-INDENT: -0.25in; mso-list: l0 level1 lfo2"><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"><SPAN style="mso-list: Ignore">2)<FONT face="Times New Roman" size=1><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></FONT></SPAN></SPAN></FONT><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">Have you compared raw DWIs and Analyze (after FSL eddy correction) DWIs?</SPAN></FONT></P>
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<div><B><FONT face=Tahoma size=2><SPAN style="FONT-WEIGHT: bold; FONT-SIZE: 10pt; FONT-FAMILY: Tahoma">From:</SPAN></FONT></B><FONT face=Tahoma size=2><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Tahoma"> <a href="mailto:mristudio-users-bounces@mristudio.org">mristudio-users-bounces@mristudio.org</a> [<A onclick="return true;Popup.composeWindow('pcompose.php?sendto=mristudio-users-bounces%40mristudio.org');; return false;" href="mailto:mristudio-users-bounces@mristudio.org" target=_blank mce_href="mailto:mristudio-users-bounces@mristudio.org"><a href="mailto:mristudio-users-bounces@mristudio.org">mailto:mristudio-users-bounces@mristudio.org</a></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">Mristudio-users@mristudio.org</a><BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> [Mristudio-users] Results using analyze format in DTIStudio</SPAN></FONT></div></DIV>
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<div><FONT face="Times New Roman" size=3><SPAN style="FONT-SIZE: 12pt">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 onclick="return true;Popup.composeWindow('pcompose.php?sendto=graeme.schwindt%40gmail.com');; return false;" href="mailto:graeme.schwindt@gmail.com" target=_blank mce_href="mailto:graeme.schwindt@gmail.com"><a href="mailto:graeme.schwindt@gmail.com">graeme.schwindt@gmail.com</a></A><BR>416.546.5453 </SPAN></FONT></div></DIV>
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