Closed leej3 closed 7 years ago
@leej3 thanks for pointing this out - this interface was only tested with Siemens dicoms.
looks like the fix should be pretty straightforward - adding a search for GE DTI vectors
when parsing the stdout - could you give it a try? And if it works, could you submit a PR?
EDIT: read my mind!
Ah, you spotted it. Great. The change has worked for me so far.
Cheers
Summary
bval and bvec files are not kept during a conversion of certain dti dicoms using the dcm2niix interface. From what I can tell this might be due the appropriate pattern not being found in the stdout of dcm2niix. This search is performed on line 307 of the dcm2nii.py interface file :
elif 'DTI gradients' in line or 'DTI gradient directions' in line: find_b = True
(https://github.com/nipy/nipype/blob/master/nipype/interfaces/dcm2nii.py, af2b7aaa60a9ab28116c0edb019a2e34c959b3d4)
Actual behavior
Using nipype to convert from dicom to nifti, both .nii.gz. and .json files are retrieved but the bvec and bval files are deleted during the post conversion clean up.
Expected behavior
DTI sequence dicoms yield nifti, json, bvec, and bval given the appropriate conversion flags
How to replicate the behavior
I can't share the DICOM, it was collected recently on a GE scanner (DISCOVERY MR750).
Script/Workflow details
Dcm2niix
Nipype
Please put URL to code or code here (if not too long). https://github.com/leej3/dti_conversion_issue
Platform details:
Please paste the output of:
python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"
The above command doesn't working (its python 2 in the container). NiPipye : 0.13.0-dev Python : 2.7 Nibabel: 2.1.0
Execution environment
Running inside the nipy/heudiconv image: sha256:8b3b92bb63ac72ced5f2f92bd9e6c9312a98ef6b503ba53f29d4623d3f8fa8e1