Dr. Xin,<br><br>Thank you for your reply. Could you please let me know after fixing this problem? <br><br>govind<br><br><div class="gmail_quote">On Wed, Feb 4, 2009 at 3:23 PM, XIN LI <span dir="ltr"><<a href="mailto:xli16@jhmi.edu">xli16@jhmi.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Govind,<br>
<br>
I am going to fix this problem. Please ignore the message. Kimap000.vtk is the Kimap you need to transform your image.<br>
<br>
<br>
Xin<br>
<div><div></div><div class="Wj3C7c"><br>
<br>
<br>
<br>
<br>
----- Original Message -----<br>
From: Varan Govind <<a href="mailto:varangovind@gmail.com">varangovind@gmail.com</a>><br>
Date: Wednesday, February 4, 2009 1:47 pm<br>
Subject: [Mristudio-users] LDDMM in LandMarker<br>
To: <a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a><br>
<br>
<br>
> Dear LandMarker Developers and Users,<br>
><br>
> I've been trying to use the LDDMM option in LandMarker to perform<br>
> intra-subject registration of T2-weighted images with b=0 images following<br>
> the procedure detailed in Dr. Mori's paper,entitled, 'Correction of B0<br>
> susceptibility induced distortion in diffusion-weighted images using<br>
> large-deformation diffeomorphic metric mapping', Magn. Reson. Imaging<br>
> 26:1294-302 (2008). Briefly, the following were performed:<br>
><br>
> Step 1: In DtiStudio (version 3.0 Beta), to correct eddy current distorion,<br>
> all DWI were registered to b=0 images using AIR and selecting<br>
> 'Affine' for<br>
> the 'Linear Transformation Approach'.<br>
><br>
> Step 2: T2-weighted and mean b=0 images were skull stripped using MRICro.<br>
><br>
> Step 3: Skull-stripped T2 (target) and b=0 images (subject) were<br>
> loaded to<br>
> LandMarker. Both the images were resampled so that they have the same<br>
> spatial resolution using 'Resample Image', prior to which, data<br>
> format of<br>
> both were changed to using 'Change Image Data Format' option (both<br>
> the<br>
> files have the same spatial resolutions, i.e., 128x128x2 mm3 resolution).<br>
><br>
> Step 4: Intensity of both the images (T2 and b=0) were adjusted using<br>
> 'Intensity Correction' option in the Volume LDDMM.<br>
><br>
> Step 5: 'Single channel' option under Volume LDDMM was selected to set<br>
> parameters for this registration process and provided my email<br>
> address and<br>
> submitted the data for remote processing.<br>
><br>
> After a few minutes, I have got an email from <a href="mailto:lddmmproc@cis.jhu.edu">lddmmproc@cis.jhu.edu</a><br>
> with an<br>
> Md5 String and an ftp link for downloading the processed data.<br>
><br>
> Step 6: To view the registered data, I copied the Md5 string from the<br>
> email<br>
> message and pasted it at 'Retrieve Results From Remote Volume LDDMM'<br>
> in<br>
> LandMarker. A little while later, I've got a message that said 'The Kimap<br>
> file cannot be found in the resultant data'. I extracted the files<br>
> from the<br>
> Results.zip file and found a non-zero size Kimap file, named as<br>
> Kimap000.vtk.<br>
><br>
> If anybody got the same message in LandMarker, 'The Kimap file cannot<br>
> be<br>
> found in the resultant data', could you please let me know how I can<br>
> see the<br>
> results?<br>
><br>
> Thank you very much in advance,<br>
><br>
> govind<br>
> University of Miami, Miami, Florida<br>
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><br>
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</blockquote></div><br>