[Mristudio-users] LDDMM in LandMarker

[Varan Govind]

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
> >
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