[Mristudio-users] LDDMM in LandMarker

[XIN LI]

Govind,

I am going to fix this problem. Please ignore the message. Kimap000.vtk is the Kimap you need to transform your image.


Xin





----- Original Message -----
From: Varan Govind <varangovind at gmail.com>
Date: Wednesday, February 4, 2009 1:47 pm
Subject: [Mristudio-users] LDDMM in LandMarker
To: mristudio-users at mristudio.org


> Dear LandMarker Developers and Users,
>  
>  I've been trying to use the LDDMM option in LandMarker to perform
>  intra-subject registration of T2-weighted images with b=0 images following
>  the procedure detailed in Dr. Mori's paper,entitled, 'Correction of B0
>  susceptibility induced distortion in diffusion-weighted images using
>  large-deformation diffeomorphic metric mapping', Magn. Reson. Imaging
>  26:1294-302 (2008). Briefly, the following were performed:
>  
>  Step 1: In DtiStudio (version 3.0 Beta), to correct eddy current distorion,
>  all DWI were registered to b=0 images using AIR and selecting 
> 'Affine' for
>  the 'Linear Transformation Approach'.
>  
>  Step 2: T2-weighted and mean b=0 images were skull stripped using MRICro.
>  
>  Step 3: Skull-stripped T2 (target) and b=0 images (subject) were 
> loaded to
>  LandMarker. Both the images were resampled so that they have the same
>  spatial resolution using 'Resample Image', prior to which, data 
> format of
>  both were changed to   using 'Change Image Data Format' option (both 
> the
>  files have the same spatial resolutions, i.e., 128x128x2 mm3 resolution).
>  
>  Step 4: Intensity of both the images (T2 and b=0) were adjusted using
>  'Intensity Correction' option in the Volume LDDMM.
>  
>  Step 5: 'Single channel' option under Volume LDDMM was selected to set
>  parameters for this registration process and provided my email 
> address and
>  submitted the data for remote processing.
>  
>  After a few minutes, I have got an email from lddmmproc at cis.jhu.edu 
> with an
>  Md5 String and an ftp link for downloading the processed data.
>  
>  Step 6: To view the registered data, I copied the Md5 string from the 
> email
>  message and pasted it at 'Retrieve Results From Remote Volume LDDMM' 
> in
>  LandMarker. A little while later, I've got a message that said 'The Kimap
>  file cannot be found in the resultant data'. I extracted the files 
> from the
>  Results.zip file and found a non-zero size Kimap file, named as
>  Kimap000.vtk.
>  
>  If anybody got the same message in LandMarker, 'The Kimap file cannot 
> be
>  found in the resultant data', could you please let me know how I can 
> see the
>  results?
>  
>  Thank you very much in advance,
>  
>  govind
>  University of Miami, Miami, Florida 
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>