[Mristudio-users] LDDMM in LandMarker

[Varan Govind]

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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