TypeError problem from monoexponential.py

[d3christ]

We are running tedana and are getting the following TypeError. Any ideas on what could be the cause?

$ tedana -d BOLD_SmokeCues_MultiTE_12.nii BOLD_SmokeCues_MultiTE_12a.nii BOLD_SmokeCues_MultiTE_12b.nii -e 13 36 58
/u/home/d/dpchrist/.local/lib/python3.6/site-packages/sklearn/utils/fixes.py:313: FutureWarning: numpy not_equal will not check object identity in the future. The comparison did not return the same result as suggested by the identity (`is`)) and will change.
  _nan_object_mask = _nan_object_array != _nan_object_array
/u/home/d/dpchrist/.local/lib/python3.6/site-packages/sklearn/externals/joblib/externals/cloudpickle/cloudpickle.py:47: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
  import imp
Traceback (most recent call last):
  File "/u/home/d/dpchrist/.local/bin/tedana", line 11, in <module>
    load_entry_point('tedana==0.0.4', 'console_scripts', 'tedana')()
  File "/u/home/d/dpchrist/.local/lib/python3.6/site-packages/tedana/workflows/tedana.py", line 447, in _main
    tedana_workflow(**vars(options))
  File "/u/home/d/dpchrist/.local/lib/python3.6/site-packages/tedana/workflows/tedana.py", line 371, in tedana_workflow
    t2s, s0, t2ss, s0s, t2sG, s0G = model.fit_decay(catd, tes, mask, masksum)
  File "/u/home/d/dpchrist/.local/lib/python3.6/site-packages/tedana/model/monoexponential.py", line 90, in fit_decay
    betas = np.linalg.lstsq(X, log_data, rcond=None)[0]
  File "/u/local/apps/python/3.6.1/lib/python3.6/site-packages/numpy-1.12.1-py3.6-linux-x86_64.egg/numpy/linalg/linalg.py", line 1961, in lstsq
    0, work, -1, iwork, 0)
TypeError: must be real number, not NoneType

[tsalo]

It looks like the problem is the argument rcond in version 1.12.1 of numpy. To replicate with that version:

import numpy as np
a = np.random.random((100, 1))
b = np.random.random((100, 10))
betas = np.linalg.lstsq(a, b, rcond=None)[0]

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/tsalo/anaconda/envs/python3/lib/python3.6/site-packages/numpy/linalg/linalg.py", line 1961, in lstsq
    0, work, -1, iwork, 0)

I think the best solution would be to update numpy. I believe that tedana requires 1.14 at minimum.

[emdupre]

Just to 👍 @tsalo's suggestion, it looks like your numpy version is likely causing the error. If you could update that library @d3christ, hopefully that will resolve the issue ! Let us know how it goes.

[d3christ]

@emdupre @tsalo
Thank you guys!
So after upgrading numpy I ran into a memory error, so I decided to upgrade all the dependencies.

I am running the same files in a hpc node and then locally on my mac. They are both taking a really long time to run and I do not know if that is normal. They are both at
...scipy/stats/stats.py:1713: FutureWarning.... then
return np.reduce(sorted[indexer] * weights, axis=axis / sumval

I would copy and paste but I am on a different computer because the tedana command seems to be taking up all of my ram lol. Is this normal?

[tsalo]

Sorry for the delay! Did it finish running at any point? In my experience, tedana takes about 20-30 minutes to finish running on a single run.

[tsalo]

@d3christ Was this ever resolved (i.e., did it finish running)? If so, I'd like to close this issue.

[jbteves]

@tsalo if we don't hear back by May 1 I'd like to propose we close this issue. I failed to mention more details in #188 but the symptoms described above were very similar to the all-cores problem I had on my server, so I would suspect that the user above had the same problem. If somebody comes along later with the same problem we can re-open this one.

[tsalo]

I think it's reasonable to close it now. The last update was a couple of months ago.