[slicer-users] BRAINSDemonWarp registration: error in saving transform and question on applying non-rigid transform to fiducial set

Dominik Meier meier at bwh.harvard.edu
Mon Nov 29 11:02:10 EST 2010


Hi Ashley

I've had success with writing deformation fields from BRAINSDemonWarp, but only via commandline and the -O option.
4D deformation fields are not yet uniformly handled in the GUI, which may have caused some of the errors you saw.

Dominik



On Nov 24, 2010, at 5:05 PM, Ashley Weaver wrote:

> Hi Andriy,
> 2. That's a good suggestion. I tried just changing the extension in the filename from .tfm to .nrrd, but it appends the File Format when I click save so the file ends up with ...Transform.nrrd.tfm and I get the same error.
> 
> Do you have a suggestion of a way around this?
> Thanks,
> Ashley
>  
> On Wed, Nov 24, 2010 at 4:56 PM, Andriy Fedorov <fedorov at bwh.harvard.edu> wrote:
> Ashley,
> 
> 1. I don't think so.
> 
> 2. I believe the transformation produced by this tool is represented
> as a deformation field, which is an image. ITK will not let you save
> an image with .tfm extension. Try specifying a valid image IO
> extension, e.g., .nrrd.
> 
> AF
> 
> 
> 
> On Wed, Nov 24, 2010 at 16:48, Ashley Weaver <aaruggle at gmail.com> wrote:
> > Hello,
> > I have 2 questions (see below). I'm running Slicer 3.6.1 on a 64-bit Linux
> > computer. Any help is appreciated! -Ashley
> > 1.  Is there a method within Slicer to apply a BRAINSDemonWarp transform to
> > a fiducial set?
> > 2.  I am having trouble saving the BRAINSDemonWarp transform.  Could someone
> > help?
> > I used the diffeomorphic registration filter type for BRAINSDemon Warp
> > registration and the results visibly look good in Slicer.  However, the
> > following error pops up when I try to save the BRAINSDemon Transform:
> > "Cannot write data file, /home.../BRAINSDemonWarpTransform.tfm. Do you want
> > to continue saving?"
> > I also get the following error in the log when trying to save:
> > Description: ERROR: In
> > /home/hayes/Slicer-3-6/Slicer3/Libs/MRML/vtkMRMLTransformStorageNode.cxx,
> > line 841
> > vtkMRMLTransformStorageNode (0x2aaab8415750): ITK exception caught writing
> > transform file: /home/.../BRAINSDemonWarp Transform4.tfm
> > itk::ImageFileWriterException (0x1c08d830)
> > Location: "void itk::ImageFileWriter<TInputImage>::Write() [with TInputImage
> > = vtkMRMLTransformStorageNode::WriteData(vtkMRMLNode*)::GridType]"
> > File:
> > /home/hayes/Slicer-3-6/Slicer3-lib/Insight/Code/IO/itkImageFileWriter.txx
> > Line: 152
> > Description:  Could not create IO object for file /home/.../BRAINSDemonWarp
> > Transform4.tfm
> >   Tried to create one of the following:
> >     MRMLIDImageIO
> >     CommandIO
> >     MGHImageIO
> >     GDCMImageIO
> >     MetaImageIO
> >     PNGImageIO
> >     VTKImageIO
> >     GiplImageIO
> >     BioRadImageIO
> >     LSMImageIO
> >     AnalyzeImageIO
> >     NiftiImageIO
> >     StimulateImageIO
> >     JPEGImageIO
> >     TIFFImageIO
> >     NrrdImageIO
> >     BMPImageIO
> >     Brains2MaskImageIO
> >     GE5ImageIO
> >   You probably failed to set a file suffix, or
> >     set the suffix to an unsupported type.
> > If it's relevant, I also get the following error in the log after running
> > the registration:
> >
> > Description: ERROR: In
> > /home/hayes/Slicer-3-6/Slicer3/Libs/MRML/vtkMRMLTransformStorageNode.cxx,
> > line 594
> > vtkMRMLTransformStorageNode (0x2aaab8415750): Grid transform with a
> > non-identity orientation matrix is not yet implemented
> >
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