phase fieldmaps not converting #7
Closed
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
this is a nibabel problem if dicom rescale values are Decimal: see nipy/nibabel#145 |
|
I pushed a test case for the nibabel PR so should hopefully get merged soon. I am closing this issue as that is the place to fix this. |
Closed
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
My phase fieldmaps are not converting. The error was:
File "build/bdist.linux-x86_64/egg/dcmstack/dcmmeta.py", line 1496, in from_dicom_wrapper
nii_img = nb.nifti1.Nifti1Image(data, affine)
File "/srv/software/python/EPD/virtualenvs/7.2/nipype0.5/lib/python2.7/site-packages/nibabel/spatialimages.py", line 317, in init
self._header.set_data_dtype(data.dtype)
File "/srv/software/python/EPD/virtualenvs/7.2/nipype0.5/lib/python2.7/site-packages/nibabel/analyze.py", line 578, in set_data_dtype
'data dtype "%s" not recognized' % datatype)
HeaderDataError: data dtype "object" not recognized
Not sure why only my phase fieldmap datatypes are "object" instead of "int16" so I added a couple lines to get it convert. I don't think its the best fix though, so any suggestions would be appreciated!