Description
cc: @jcfr @lassoan @pieper
Nifti1 has scl_slope and scl_inter. The equivalent attributes in the NRRD are oldmin and oldmax as if:
# define oldmin and oldmax when scl_slope and scl_inter are present
img= nibabel.load('filename')
dtype= img.header.get_data_dtype().name
scl_slope= img.dataobj.slope
scl_inter= img.dataobj.inter
if scl_slope!=1.0 or scl_inter!=0:
info= np.iinfo(dtype)
oldmin= info.min*scl_slope+scl_inter
oldmax= info.max*scl_slope+scl_inter
print(f'old min: {oldmin}')
print(f'old max: {oldmax}')
(you can also look at this commit by Chris Rorden)
Actual behavior
However, after I defined old min and old max in the NRRD header, the data reported in Slicer aren't scaled. The difference becomes stark when you load both NIFTI and NRRD image in Slicer. NIFTI voxels are scaled while NRRD aren't. On the other hand, fslview, NIBABEL both report the data after scaling.
Expected behavior
So, we should report NRRD data after scaling them as follows:
find scl_slope and scl_inter from above and
scaled_data= unscaled_data*scl_slope+ scl_inter
Additional Information
Work with the following public data: the T1_echo*.nii.gz have scaling present in the NIFTI.
http://people.cas.sc.edu/rorden/SW/dcm2niix/odd/multiechotest_Philips_Vanderbilt.zip
dcm2niix should do the DICOM-->NIFTI conversion for you. Then you can use conversion repository to convert NIFTI-->NHDR
Description
cc: @jcfr @lassoan @pieper
Nifti1 has scl_slope and scl_inter. The equivalent attributes in the NRRD are oldmin and oldmax as if:
(you can also look at this commit by Chris Rorden)
Actual behavior
However, after I defined old min and old max in the NRRD header, the data reported in Slicer aren't scaled. The difference becomes stark when you load both NIFTI and NRRD image in Slicer. NIFTI voxels are scaled while NRRD aren't. On the other hand, fslview, NIBABEL both report the data after scaling.
Expected behavior
So, we should report NRRD data after scaling them as follows:
find scl_slope and scl_inter from above and
scaled_data= unscaled_data*scl_slope+ scl_inter
Additional Information
Work with the following public data: the T1_echo*.nii.gz have scaling present in the NIFTI.
http://people.cas.sc.edu/rorden/SW/dcm2niix/odd/multiechotest_Philips_Vanderbilt.zip
dcm2niix should do the DICOM-->NIFTI conversion for you. Then you can use conversion repository to convert NIFTI-->NHDR