<div>Hello Hangyi,</div>
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<div>My apologies for hijacking Weihong's thread, but I would also be very interested in a command line version of the program. Can you please let me know where I can find it. I would be happy to report back bug reports to help improve it.</div>
<div> </div>
<div>Thank you,</div>
<div>Jeff<br><br></div>
<div class="gmail_quote">On Thu, Aug 19, 2010 at 7:04 AM, susumu mori <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hi Weihong,<br><br>
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<div>1. After registering the DWIs to b0, is there anyway to get some quantification about the motion?It would be great if we can get the frame by frame motion "magnitude" (rotation, translation, skew) data in the form of a text file. Is there a existing function available in DTIStudio that can allow me to do that? </div>
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<div><br>Please see <a href="https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2" target="_blank">https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2</a>. There you can find a *.doc file explaining how you can check the motion correction results. In reality, the cross-contrast registration like b0-DWI is difficult and it is difficult to expect perfect registration. However, as the file explains, mutual information, although it takes longer, tends to perform better. AIR also has a strong dependence on threshold value.<br>
<br>We are working on quantitative reporting of the registration results. Currently there is an option to save the transformation matrix in the text format. When you start AIR, at the bottom of the AIR window, there is "Save transformation matrix" in the "Other" section.<br>
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<div>2. Is there a beta version of the software that can do some batch work? I understand the quality checking for bad frame/slice/pixel always needs human decision, as you have mentioned before. What about batch job for motion/eddy current correction, or other procedure that may not need as much human expertise?</div>
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<div><br>Hangyi has a command-line version of the software. It may not support all the functions, but please contact him.<br> <br></div>
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<div>Thanks in advance</div>
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<div>Weihong</div>
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<div> </div>Weihong Yuan, Ph.D.<br>Research Assistant Professor/McLaurin Fellow<br>Pediatric Neuroimaging Research Consortium<br>Imaging Research Center, Dept. of Radiology<br>Cincinnati Children's Hospital Research Foundation<br>
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