DWIConvert error when trying to convert DICOM to NRRD

[felixveysseyre]

Hello,

I'm currently trying to convert a DICOM directory into a NRRD file trough your slicer plugin DWIConvert.

When I run the command line:
./DWIConvert --inputDicomDirectory /home/felix/Downloads/1020_DICOMS --outputDirectory /home/felix/Downloads/Test --outputVolume test.nrrd

I have the following report:
terminate called without an active exception
Aborted (core dumped)

I am using the latest version of Slicer.

Thanks,
Felix

[Chaircrusher]

I'd be glad to have a look at the problem if I can get access to the dataset. Can you anonymize it and upload it?

If I had to guess, I'd say it was missing DICOM tags that are needed to extract the gradient vectors.

Are you trying to convert a non-DWI Dicom Series? Slicer has other DICOM plugins that can do that.

[felixveysseyre]

1020_DICOMS.tar.gzhttps://docs.google.com/a/kitware.com/file/d/0B-1wLMrsF8gnUElxalRHejdTMFU/edit?usp=drive_web

Here we'are !

To be honest I do not know very much, I just sit in Kitware as an intern

Thank you for your time,

Felix.

On Wed, Jul 17, 2013 at 4:53 PM, Kent Williams notifications@github.comwrote:

I'd be glad to have a look at the problem if I can get access to the
dataset. Can you anonymize it and upload it?

If I had to guess, I'd say it was missing DICOM tags that are needed to
extract the gradient vectors.

Are you trying to convert a non-DWI Dicom Series? Slicer has other DICOM
plugins that can do that.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/57#issuecomment-21144028
.

[Chaircrusher]

That DICOM series is missing the tags needed to identify the vendor, without which DWIConvert will not work. It is also not a DWI (Diffusion Weighted Imaging) series which DWIConvert is meant to convert.

[felixveysseyre]

Ok, I was misled by the old module name.

Could you advise me a module?

Thanks a lot.

[Chaircrusher]

After further testing I think I have a solution for you.

1. I've made changes to DWIConvert to do a better job with non-DWI DICOM datasets. This can be downloaded here: https://github.com/BRAINSia/BRAINSTools
2. A big part of the problem with that dataset is that it has a total of 75 DICOM files, but only the first 74 are part of the volume you want to load. The 75th is a sort of overview scan or thumbnail of the set; it is oriented differently than the rest of the slices. This last slice needs to be removed from the DICOM directory, in order for the ImageFileReader to handle the dataset correctly.
3. It isn't built as a standard part of BRAINSTools (or Slicer) but if you build BRAINSTools, you can use CMake to add ConvertBetweenFileFormats to the utilities built. It can handle loading DICOM series and writing them out to any file format supported by ITK.

Unfortunately for you, this is a 'some assembly required' thing: The version of DWIConvert that comes in the Slicer package won't help you.

[hjmjohnson]

I think that this has been resolved on the BRAINSia builds. We can not integrate with Slicer until after the RSNA conference in late November.