Deprecation error #36
Description
I'm using the Docker image (via singularity) for v0.1.4 and am attempting to write fixel stats and get the following:
singularity exec --containall -B $PWD:$PWD /groups/adamraikes/singularity_images/modelarray_confixel_0.1.4.sif fixelstats_write --index-file fixel_stats/fd_smooth/index.mif --directions-file fixel_stats/fd_smooth/directions.mif --cohort-file modelarray_inputs/full_dataset_fd.csv --relative-root $PWD --input-hdf5 modelarray_output/interaction_models/full_dataset_fd.h5 --output-dir modelarray_output/interaction_models/full_dataset_fd --analysis-name results
WARNING: Output directory exists
Traceback (most recent call last):
File "/usr/local/bin/fixelstats_write", line 8, in <module>
sys.exit(h5_to_fixels())
File "/usr/local/lib/python3.8/dist-packages/confixel/fixels.py", line 306, in h5_to_fixels
h5_to_mifs(example_mif, h5_input, analysis_name, out_fixel_dir)
File "/usr/local/lib/python3.8/dist-packages/confixel/fixels.py", line 247, in h5_to_mifs
nifti2_img, _ = mif_to_nifti2(example_mif)
File "/usr/local/lib/python3.8/dist-packages/confixel/fixels.py", line 45, in mif_to_nifti2
data = nifti2_img.get_data().squeeze()
File "/usr/local/lib/python3.8/dist-packages/nibabel/deprecator.py", line 185, in deprecated_func
raise error_class(message)
nibabel.deprecator.ExpiredDeprecationError: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
Only index.mif and directions.mif are written to the output folder.
EDIT: Outputs are created using v0.1.3. Also, this error does not occur for volumestats_write