[Mristudio-users] LDDMM in LandMarker

[XIN LI]

Govind,

We have fixed the problem. You wouldn't get the warning message any more.


Xin

----- Original Message -----
From: Varan Govind <varangovind at gmail.com>
Date: Monday, February 9, 2009 5:14 pm
Subject: Re: [Mristudio-users] LDDMM in LandMarker
To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <mristudio-users at mristudio.org>


> Dr. Xin,
>  
>  Thank you for your reply. Could you please let me know after fixing this
>  problem?
>  
>  govind
>  
>  On Wed, Feb 4, 2009 at 3:23 PM, XIN LI <xli16 at jhmi.edu> wrote:
>  
>  > 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
>  > > _______________________________________________
>  > >  Mristudio-users mailing list
>  > >  Mristudio-users at mristudio.org
>  > >
>  > _______________________________________________
>  > Mristudio-users mailing list
>  > Mristudio-users at mristudio.org
>  > 
>  > 
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