open-discussion
open-discussion > RE: to get the bvals/bvecs from DTI DICOM data?
Jan 11, 2012 03:01 PM | Nolan Nichols
RE: to get the bvals/bvecs from DTI DICOM data?
Hi ConXZ,
If you want to use python to access the bvecs/bvals directly from the DICOM header, I suggest using the pydicom package (http://code.google.com/p/pydicom), but the script you use wil depend on what scanner you use and which DICOM format you are using (e.g., Classic vs. Multi-frame DICOM).
Manufacturers (Philips, GE, Siemens, etc.) use different DICOM tags to store bvecs/bvals, and even a single manufacturer may store the bvec/bvals differently for a given DICOM format.
For example, I normally use dcm2nii (http://www.nitrc.org/projects/mricron) to get the bvecs/bvals from our Philips scans in the classic DICOM format, but I am now working with the Philips Multi-Frame DICOM format called "Enhanced DICOM" and dcm2nii does not output the bvecs/bvals files for this format. As a work around I wrote a script using pydicom to extract the bvecs/bvals. Its not pretty, but hopefully it gives you an idea for where to start: https://github.com/UW-IBIC/ibicUtils
Cheers,
Nolan
If you want to use python to access the bvecs/bvals directly from the DICOM header, I suggest using the pydicom package (http://code.google.com/p/pydicom), but the script you use wil depend on what scanner you use and which DICOM format you are using (e.g., Classic vs. Multi-frame DICOM).
Manufacturers (Philips, GE, Siemens, etc.) use different DICOM tags to store bvecs/bvals, and even a single manufacturer may store the bvec/bvals differently for a given DICOM format.
For example, I normally use dcm2nii (http://www.nitrc.org/projects/mricron) to get the bvecs/bvals from our Philips scans in the classic DICOM format, but I am now working with the Philips Multi-Frame DICOM format called "Enhanced DICOM" and dcm2nii does not output the bvecs/bvals files for this format. As a work around I wrote a script using pydicom to extract the bvecs/bvals. Its not pretty, but hopefully it gives you an idea for where to start: https://github.com/UW-IBIC/ibicUtils
Cheers,
Nolan
Threaded View
| Title | Author | Date |
|---|---|---|
| xiangzhen kong | Jan 11, 2012 | |
| Nolan Nichols | Jan 11, 2012 | |
| vania karami | Jan 25, 2013 | |
| Cin Hovcat | Jan 25, 2013 | |
| Marco Antonio Gomes Del Aquilla | Jan 11, 2012 | |
| Cin Hovcat | Jan 25, 2013 | |
| Torsten Rohlfing | Jan 11, 2012 | |
