It is a common practice to perform 12-mode affine before tensor calculation. If your scanner doesn't have noticeable eddy current (like many modern Siemens), you can do 6-mode rigid just for motion correction.<br><br><div class="gmail_quote">
On Mon, Jun 25, 2012 at 4:18 PM, Santosh Yadav <span dir="ltr"><<a href="mailto:santoshyadav20076@gmail.com" target="_blank">santoshyadav20076@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>Dear Dr Hangyi,</div><div> </div><div>Lot of thanks for great response.</div><div> </div><div>I have another question regarding DTI processing.</div><div> </div><div>I am processing the DTI data acquired from Siemens 3T for LDDMM, Is it necessary/important step to do the Automatic image registration using a 12-mode affine transformation before tensor calculation?</div>
<div> </div><div>As I read the articles, It is important step for motion and eddy current distortion correction in the DTI data.</div><div> </div><div>Ref. </div><div>1. Neuroimage 2009; 47(2): 618-627</div><div>2. <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Jiang%20H%5BAuthor%5D&cauthor=true&cauthor_uid=16413083" target="_blank"><span style="color:windowtext;text-decoration:none"><font size="3" face="Calibri">Jiang H</font></span></a><font size="3" face="Calibri">
Comput Methods Programs Biomed. 2006, 81(2):106-16</font></div><div> </div><div> </div><div>With Best Regards</div><div> </div><div>Santosh</div><div> </div><div><br> </div><div class="gmail_quote">On Mon, Jun 25, 2012 at 4:50 AM, Hangyi Jiang <span dir="ltr"><<a href="mailto:hjiang@jhmi.edu" target="_blank">hjiang@jhmi.edu</a>></span> wrote:<br>
<blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote"><br>
there is no standard answer for your question, it depends on original dataset. the following recommends are just for your reference:<br>
<br>
if your dataset has only few diffusion orientations (e.g. less than 8), you may try:<br>
manual image quality check + standard linear fitting or outlier pixel rejection method;<br>
<br>
if you have only few subjects to study, you way try:<br>
manual image quality check + standard linear fitting;<br>
<br>
if your dataset have a lot of DW orientations (e.g. more than 15), you can try:<br>
outlier slice rejection method;<br>
<br>
if you find motion artifact, you can use AIR based method.<br>
<br>
and......<br>
<br>
best,<br>
<br>
<br>
hangyi<br>
<br>
<br>
<br>
<br>
<br>
<br>
or outlier pixel rejection method;<br>
<br>
<br>
________________________________<br>
From: <a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a> [<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>] on behalf of Santosh Yadav [<a href="mailto:santoshyadav20076@gmail.com" target="_blank">santoshyadav20076@gmail.com</a>]<br>
Sent: Sunday, June 24, 2012 4:24 AM<br>
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
Subject: [Mristudio-users] Tensor calculation<div><div class="h5"><br>
<div><div><br>
Hello DTI Experts,<br>
<br>
I want to know which method is good for tensor calculation using DTI-Studio for LDDMM.<br>
<br>
In DTI-Studio, for tensor calculation there are four methods:<br>
<br>
1. Standard linear registration<br>
2. Automatic outlier SLIC rejection<br>
3. Automatic outlier pixel rejection method<br>
4. AIR for theory-original DWI pair with using a 12-mode affine transformation (Woods et al., 1998)<br>
<br>
I read few articles which described the tensor calculation by using AIR for theory-original DWI pair Method (Method 4) (Neuroimage 2009; 47(2): 618-627, Neuroimage 2009; 46(2): 486-499), is this method having any advantage over Automatic outlier pixel rejection method?<br>
<br>
With Best Regards<br>
<br>
<br>
--<br>
With Best Regards,<br>
<br>
Neuroscience and MR Research Program<br>
<br>
Department of Medicine, Queen's Medical Center<br>
<br>
University of Hawaii<br>
<br>
1356 Lusitana Street, 7th Floor, Honolulu, HI 96813<br>
<br>
Phone No. <a href="tel:808-220-7152" value="+18082207152" target="_blank">808-220-7152</a><br>
<br>
Fax No. <a href="tel:808-545-8970" value="+18085458970" target="_blank">808-545-8970</a><br>
<br>
<br>
<br>
</div></div></div></div></blockquote></div><div class="HOEnZb"><div class="h5"><br><br clear="all"><br>-- <br><div style="margin:0in 0in 0pt"><span style="line-height:115%;font-size:12pt"><font face="Calibri">With Best Regards,</font></span></div>
<div style="margin:0in 0in 0pt"><span style="line-height:115%;font-size:12pt"></span> </div>
<div style="margin:0in 0in 0pt"><span style="line-height:115%;font-size:12pt"><font face="Calibri">Neuroscience and MR Research Program</font></span></div>
<p style="margin:0in 0in 0pt"><span style="line-height:115%;font-size:12pt"><font face="Calibri">Department of Medicine, Queen's Medical Center</font></span></p>
<p style="margin:0in 0in 0pt"><span style="line-height:115%;font-size:12pt"><font face="Calibri">University of Hawaii</font></span></p>
<p style="margin:0in 0in 0pt"><span style="line-height:115%;font-size:12pt"><font face="Calibri">1356 Lusitana Street, 7th Floor, Honolulu, HI 96813 </font></span></p>
<p style="margin:0in 0in 0pt"><span style="line-height:115%;font-size:12pt"><font face="Calibri">Phone No. <a href="tel:808-220-7152" value="+18082207152" target="_blank">808-220-7152</a></font></span></p>
<p style="margin:0in 0in 0pt"><span style="line-height:115%;font-size:12pt"><font face="Calibri">Fax No.<span> </span><a href="tel:808-545-8970" value="+18085458970" target="_blank">808-545-8970</a></font></span></p>
<p> </p><br>
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