questions > Enhanced Dicom Siemens Vida XA11 bval/bvec files
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Feb 22, 2019  02:02 AM | egourieux
Enhanced Dicom Siemens Vida XA11 bval/bvec files
Dear all,

Recently we received Enhanced Dicom from a Siemens Vida (software version syngo_MR_XA11) and we had issues with these dicom.
One of the issue is that with dcm2niix the 'bval'/'bvec' files are not extracted from DTI series.
I suppose it is because Siemens XA format no longer includes the proprietary Siemens CSA header ?
However it seems that b-value are in the dicom tag (0019, 100c) and bvec in the dicom tag (0019, 100e).

I know some change have been already made in dcm2niix to add some information in the json file for XA10 software version (https://github.com/rordenlab/dcm2niix/is... ). In the same way, is it planned to do some developments to allow the extraction of the bvec and bval files from enhanced dicom of the software version syngo_MR_XA11 ?

Thanks,


Emmanuelle
Feb 22, 2019  04:02 AM | Chris Rorden
RE: Enhanced Dicom Siemens Vida XA11 bval/bvec files
dcm2niix can handle Siemens Vida XA10/XA11 data. The general method is described here. You may want to look at issues 236 and 240. For other Siemens DICOM we extract the DTI bvec/bval from the CSA header. But for all the Vida data I have seen they now use the public tags 0018,9089 and 0018,9087. If you use dcmdump on a set of data you should see fields like this:

(0018,9089) FD -0.20342215895652771\-0.51398676633834839\-0.8333289623260498 # 24, 3 DiffusionGradientOrientation
(0018,9087) FD 1000 # 8, 1 DiffusionBValue

I have only seen XA10 data and simulated XA11 data. I am unaware of the use of tags 0019,100c and 0019,100e. Can you please make sure the publc tags (which start with an even number are not present). I would also suggest making sure you are using the most recent release of dcm2niix (you can even try out the more recent development branch). Also, it is critical that you save to enhanced DICOM without selecting the mosaic format or the de-identification At least with XA10 selecting either of those options would strip the diffusion tags from your data.

If the problem persists, open a Github issue.
Feb 22, 2019  08:02 AM | Chris Rorden
RE: Enhanced Dicom Siemens Vida XA11 bval/bvec files
I have generated a new Github issue to address this. I note that Siemens recommends you export to enhanced DICOM. However, at least with XA11 the diffusion information is still preserved (though in private tags). Can you please test the latest development release (v1.0.20190222) and close the Github issue if it resolves your issue:

$ git clone --branch development https://github.com/rordenlab/dcm2niix.gi...
$ cd dcm2niix/console
$ make
$ ./dcm2niix

You can also compile on Windows, but I usually just go to the Development branch Github page, click the AppVeyor button and get the most recently compiled 'Artifact'

While I do not expect any issues, given the fact you are using a new system with a new feature, I would suggest you carefully validate the b-vectors generated by your sequence. You can download the "dedicated document" from the wiki that describes this.
Feb 25, 2019  02:02 AM | egourieux
RE: Enhanced Dicom Siemens Vida XA11 bval/bvec files
Your Github issue resolves my issue, thank you very much for your quick answer.