[Mristudio-users] LDDMM in LandMarker

[Varan Govind]

Dr. Xin,

Thank you for your quick response.

govind

On Tue, Feb 10, 2009 at 10:08 AM, XIN LI <xli16 at jhmi.edu> wrote:

> 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
> >  > >
> >  > _______________________________________________
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> >  > Mristudio-users at mristudio.org
> >  >
> >  >
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> >
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