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arielletambini / denoiser

Nuisance removal tool for fMRI data
Apache License 2.0
53 stars 18 forks source link

RuntimeWarning: Divide by zero #42

Open manzouri opened 2 years ago

manzouri commented 2 years ago

Hi , I run the denoiser and get the output file but not the html report due to the following error:

Computing dvars... /home/amir/.local/lib/python3.8/site-packages/numpy/lib/shape_base.py:379: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. res = asanyarray(func1d(inarr_view[ind0], *args, *kwargs)) /home/amir/.local/lib/python3.8/site-packages/numpy/lib/shape_base.py:402: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. buff[ind] = asanyarray(func1d(inarr_view[ind], args, *kwargs)) Traceback (most recent call last): File "run_denoise.py", line 462, in denoise(img_file, tsv_file, out_path, col_names, hp_filter, lp_filter, out_figure_path) File "run_denoise.py", line 316, in denoise temp = nac.compute_dvars(in_file=in_file, in_mask=mask_file)[1] File "/home/amir/.local/lib/python3.8/site-packages/nipype/algorithms/confounds.py", line 1079, in compute_dvars func_diff / np.array([diff_sdhat] func_diff.shape[-1]).T RuntimeWarning: divide by zero encountered in true_divide

maxhenneke commented 1 year ago

I am getting this same error. Did you end up finding a solution?

manzouri commented 1 year ago

@maxhenneke , Unfortunately No. I was hoping for an update from @arielletambini