questions
questions > RE: Extracting bvals/bvecs from dwi missing Siemens ASCII header "ie the ASCCONV text file'
Aug 15, 2018 08:08 PM | Chris Rorden
RE: Extracting bvals/bvecs from dwi missing Siemens ASCII header "ie the ASCCONV text file'
There is no vendor agnostic standard for reading gradient
directions from DICOM images. For Siemens data we typically extract
bvals/bvecs by reading the proprietary CSA header. These fields are populated both by the vendor supplied sequences,
as well as all the research sequences I have seen (e.g. the CMRR
sequences). I suspect that the issue is that you have run your data
through an anonymization scheme that has removed the CSA headers,
that contain crucial details for the BIDS header. I suggest you
look at the providence of your images - the raw DICOMs from the
scanner will contain these. You want to update your pipeline to
preserve these details. For the record, dcm2niix reads the stable
binary portion of the CSA header, rather than the ASCII
portion.
You may want to examine your DICOM header (you can do this with the "-v 2" option in dcm2niix). The one hope is that your data still has tags 0019;000C and 0019;000D intact - in theory this would allow you to reconstruct the bval/bvec data. However, I suspect the tool that removed the CSA header also removed these. Even if you have these, other critical information is in the CSA header (e.g. slice timing).
You may want to examine your DICOM header (you can do this with the "-v 2" option in dcm2niix). The one hope is that your data still has tags 0019;000C and 0019;000D intact - in theory this would allow you to reconstruct the bval/bvec data. However, I suspect the tool that removed the CSA header also removed these. Even if you have these, other critical information is in the CSA header (e.g. slice timing).
Threaded View
Title | Author | Date |
---|---|---|
Karl Zimmerman | Aug 15, 2018 | |
Chris Rorden | Aug 15, 2018 | |
Karl Zimmerman | Aug 16, 2018 | |