users > File format and registration problem
Mar 23, 2011  04:03 PM | Thomas Templier
File format and registration problem
Hello,

I'm doing my first steps with CMTK and have several problems.

File format :

-- I'm using .tif files of confocal images. Some have one channel, and some have several channels (image[0:100] red channel, and image[101:200] green channel for example). The only converter tool I've found that can convert a .tif in a file read by CMTK is ImageJ that converts a .tif in a .nrrd file. Is it a good solution ?

Registration : I've tried to use the affine and the nonrigid registration implemented in CMTK with my two .nrrd files.

-- when I use like in the tutorial
registration --initxlate --dofs 6,9 --auto-multi-level 4 -o affine.xform ref.nrrd flt.nrrd
   I have the following :
WARNING : the following command line arguments were not used: --auto-öulti-level 4 -o affine.xform ref.nrrd flt.nrrd
Unknown option: --auto-multi-level [argument#0]
-- if I use
warp -o ffd40.xform --grid-spacing 40 --initial affine.xform ref.nii flt.nii
then I have
The file/directory affine.xform does not seem to be in a supported transformation format

So thank you for your help. I hope there are not too stupid questions, otherwise feel free to indicate me some tutorials I've missed.



Thomas
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TitleAuthorDate
File format and registration problem
 Thomas Templier Mar 23, 2011
Torsten Rohlfing Mar 28, 2011
Thomas Templier Mar 30, 2011
Torsten Rohlfing Mar 30, 2011
Thomas Templier Apr 4, 2011
Torsten Rohlfing Apr 4, 2011
Thomas Templier Apr 4, 2011
Thomas Templier May 4, 2011
Greg Jefferis May 4, 2011
Torsten Rohlfing Mar 23, 2011
Thomas Templier Mar 24, 2011
Torsten Rohlfing Mar 24, 2011
Thomas Templier Mar 25, 2011
Torsten Rohlfing Mar 25, 2011
Thomas Templier Mar 27, 2011
Torsten Rohlfing Mar 27, 2011
Torsten Rohlfing Mar 25, 2011
Greg Jefferis Mar 25, 2011
Greg Jefferis Mar 24, 2011
Torsten Rohlfing Mar 23, 2011