questions > dcm2nii: no bvals/bvecs with files from GE scanner
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Nov 6, 2020  02:11 PM | Clara Weber
dcm2nii: no bvals/bvecs with files from GE scanner
Hi, 

I used dcm2nii for DTI images that were acquired in different scanners. For datasets from Siemens scanners, I get Nifti files as well as bvals and bvecs (as required for further procession), but for files from GE scanners, dcm2nii does not produce bvals and bvecs. It would be great if someone has an idea how to get the bvals and bvecs files. 
This is what I already found: apparently GE scanners save some information under other tags than Siemens scanners do (https://www.na-mic.org/wiki/NAMIC_Wiki:D...), but I do not know how to retrieve this information. 

Thank you in advance, 
Clara
Nov 6, 2020  03:11 PM | Chris Rorden
RE: dcm2nii: no bvals/bvecs with files from GE scanner
Please make sure you are using the latest version of dcm2niix (v1.0.20201102), which improves support for GE meta data
  https://github.com/rordenlab/dcm2niix/releases/tag/v1.0.20201102
I am well aware of the NAMIC DTI web page (I am a contributor). You can find additional details on how dcm2niix supports GE data here:
  https://github.com/rordenlab/dcm2niix/tree/master/GE

Also, please make sure that your DICOMs are direct from GE. For example, the ABCD study creates their own DICOM images from data that is acquired on GE scanners, and their format does not include much of the rich meta data useful for analyses. This is a limitation of the DICOM files provided by the ABCD team, not of dcm2niix.
Nov 10, 2020  07:11 PM | Clara Weber
RE: dcm2nii: no bvals/bvecs with files from GE scanner
Thank you for your reply and advice!

Unfortunately I couldn't get the respective files with the latest version of dcm2nii. As you suggested, I assume there's a limitation to the DICOM files themselves. 
Nevertheless, I want to thank you for your advice and contribution to this very helpful tool.
Nov 10, 2020  08:11 PM | Chris Rorden
RE: dcm2nii: no bvals/bvecs with files from GE scanner
OK, feel free to share the problematic set by sending a link to the file from DropBox/GoogleDrive to my private email. Alternatively, you can work with your GE Research Collaboration Manager. It is their job to help users with issues like this.