saving, loading and using vector field volumes

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saving, loading and using vector field volumes

annikajakobi
Hi all,

I have a problem with saving and reading back in the vector field volumes I got from a demon registration.

I cannot save them at all in .tfm, .txt, .m . But I can save them as .nrrd files. That is fine for me. But when I close the program and reload the saved data (as volumes) I only get a field with zeros: in the volume module min and max are shown as zeros. This is confirmed when I try to apply the deformation field as such (in the resample DWI volume module as displacement): the data stays unchanged.

I tried to read in the .nrrd with MATLAB, and this tells me that the .nrrd file is a 4D volume (with 256x256x110x3), and the datapoints are not zero. The same is valid when I read statistics with plastimatch: there are definetly nonzeros in that file. I converted it from .nrrd to .mha with plastimatch and reloaded that to 3DSlicer and get an image with nice colors, so: nonzeros there as well. But I cannot use the .mha file as vector field volume for the transformation.

Another thing that is confusing: plastimatch does not recognize the .nrrd file as vector field at all. The statistic option gives me the result you usually get for a 3D volume (MIN, MAX, AVE, NONZERO, NUMVOX), all nicely non zero but not as vectors.

Does anyone know, what the problem might be and how I can solve it?
What I need would be: saving the vector field volume, reloading it and USING it on CT datasets and dose datasets.

The version I use is the
4.2.2-1 r21513

Thanks!!

Cheers,
Annika

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saving, loading and using vector field volumes

annikajakobi
Hi all,

I still have a problem with saving and reading back in the vector field volumes I got from a demon registration.

I cannot save them at all in .tfm, .txt, .m . But I can save them as .nrrd files. That is fine for me. But when I close the program and reload the saved data (as volumes) I only get a field with zeros: in the volume module min and max are shown as zeros. This is confirmed when I try to apply the deformation field as such (in the resample DWI volume module as displacement): the data stays unchanged.

I tried to read in the .nrrd with MATLAB, and this tells me that the .nrrd file is a 4D volume (with 256x256x110x3), and the datapoints are not zero. The same is valid when I read statistics with plastimatch: there are definetly nonzeros in that file. I converted it from .nrrd to .mha with plastimatch and reloaded that to 3DSlicer and get an image with nice colors, so: nonzeros there as well. But I cannot use the .mha file as vector field volume for the transformation.

Another thing that is confusing: plastimatch does not recognize the .nrrd file as vector field at all. The statistic option gives me the result you usually get for a 3D volume (MIN, MAX, AVE, NONZERO, NUMVOX), all nicely non zero but not as vectors.

Does anyone know, what the problem might be and how I can solve it?
What I need would be: saving the vector field volume, reloading it and USING it on CT datasets and dose datasets.

The version I use is the
4.2.2-1 r21513

Thanks!!

Cheers,
Annika

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Re: saving, loading and using vector field volumes

Sharp, Gregory C.
Hi Annika,
 
Thank you for the report.  I tried to reproduce, and also got bad results. 
Slicer crashes when I try to load the 4D nrrd.  Clearly something is wrong.
 
So...I'm going to update to my Slicer to svn head, and see if the problem is still
existing in latest version.  Once the re-compile is complete, I'll report back.
 
Also, thanks for the report about "plastimatch stats" bug which interprets 4D nrrd
as image instead of vector field.  I will fix that.
 
One big problem is that the 4D image format is underspecified.  It might be a vector
field, or it might be an RGB volume, or something else.  We should find a way to encode the
semantic meaning of the image in the metadata, so it can properly be interpreted
as a vector field when it is loaded.  I've opened a ticket for this second item.
 
 
Greg
 

From: [hidden email] [mailto:[hidden email]] On Behalf Of [hidden email]
Sent: Thursday, April 18, 2013 2:19 AM
To: [hidden email]
Subject: [slicer-users] saving, loading and using vector field volumes

Hi all,

I still have a problem with saving and reading back in the vector field volumes I got from a demon registration.

I cannot save them at all in .tfm, .txt, .m . But I can save them as .nrrd files. That is fine for me. But when I close the program and reload the saved data (as volumes) I only get a field with zeros: in the volume module min and max are shown as zeros. This is confirmed when I try to apply the deformation field as such (in the resample DWI volume module as displacement): the data stays unchanged.

I tried to read in the .nrrd with MATLAB, and this tells me that the .nrrd file is a 4D volume (with 256x256x110x3), and the datapoints are not zero. The same is valid when I read statistics with plastimatch: there are definetly nonzeros in that file. I converted it from .nrrd to .mha with plastimatch and reloaded that to 3DSlicer and get an image with nice colors, so: nonzeros there as well. But I cannot use the .mha file as vector field volume for the transformation.

Another thing that is confusing: plastimatch does not recognize the .nrrd file as vector field at all. The statistic option gives me the result you usually get for a 3D volume (MIN, MAX, AVE, NONZERO, NUMVOX), all nicely non zero but not as vectors.

Does anyone know, what the problem might be and how I can solve it?
What I need would be: saving the vector field volume, reloading it and USING it on CT datasets and dose datasets.

The version I use is the
4.2.2-1 r21513

Thanks!!

Cheers,
Annika

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slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject