# PSI, frequency bands, and edge artifacts

**URL:** <https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308>\
**Category:** Mailing List Archive (read-only)\
**Tags:** list-archive\
**Created:** [September 2, 2020, 3:41pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308 "2020-09-02T15:41:53Z")\
**Posts on this page:** 17\
**Page:** 1

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [September 2, 2020, 3:41pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/1 "2020-09-02T15:41:53Z")

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Dear MNE Community,

When you run PSI (or other connectivity measures) on very short epochs within a given frequency band (using fmin and fmax rather than filtering beforehand), how does the function limit to those frequencies? Is there still a risk of introducing edge artifacts? Is there a common approach to quantify this risk?

Thank you,  
Josh

---

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [September 2, 2020, 7:19pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/2 "2020-09-02T19:19:38Z")

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hi,

I don't reallly know. I would try a simulation to see how it behaves.

maybe someone else has more experience

Alex

---

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**Post date:** [September 2, 2020, 10:58pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/3 "2020-09-02T22:58:20Z")

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Hi all,  
I am attempting to follow upgrade instructions. I was able to upgrade  
conda, and I succeeded in using curl to get the yml file.  
However, when I try the conda env update, I eventually get an error when  
the update gets to dipy. See below. Any suggestions?

Thanks for your help,  
Megan

conda env update --file environment.yml  
Using Anaconda Cloud api site [https://api.anaconda.org](https://api.anaconda.org)  
Fetching package metadata ...........  
Solving package specifications: .  
...  
ERROR: Invalid requirement: 'dipy --only-binary dipy'

conda --version && python --version  
conda 4.3.30  
Python 3.8.5

Here is the contents of my environment.yml file:

name: mne  
channels:  
- defaults  
dependencies:  
- python\>=3.8  
- pip  
- numpy  
- scipy  
- matplotlib  
- numba  
- pandas  
- xlrd  
- scikit-learn  
- h5py  
- pillow  
- statsmodels  
- jupyter  
- joblib  
- psutil  
- numexpr  
- traits  
- pyface  
- traitsui  
- imageio  
- tqdm  
- spyder-kernels  
- pip:  
&nbsp;&nbsp;- mne  
&nbsp;&nbsp;- imageio-ffmpeg\>=0.4.1  
&nbsp;&nbsp;- vtk\>=9.0.1  
&nbsp;&nbsp;- pyvista\>=0.24  
&nbsp;&nbsp;- pyvistaqt  
&nbsp;&nbsp;- mayavi  
&nbsp;&nbsp;- PySurfer[save\_movie]  
&nbsp;&nbsp;- dipy --only-binary dipy  
&nbsp;&nbsp;- nibabel  
&nbsp;&nbsp;- nilearn  
&nbsp;&nbsp;- neo  
&nbsp;&nbsp;- python-picard  
&nbsp;&nbsp;- PyQt5\>=5.10,\<5.14; platform\_system == "Darwin"  
&nbsp;&nbsp;- PyQt5\>=5.10; platform\_system != "Darwin"

MEG Technician  
The Mind Research Network  
1101 Yale Blvd. NE  
Albuquerque, New Mexico 87106  
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**Post date:** [September 2, 2020, 11:53pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/4 "2020-09-02T23:53:06Z")

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HI all,  
I'm wondering if this is an error because I already have things installed.  
The dipy page says to uninstall dipy before installing using pip.  
Are there separate instructions for upgrades? I realized I'm trying to  
follow install instructions.

> > > import dipy  
> > > dipy.\_\_file\_\_

'/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/lib/python3.5/site-packages/dipy/\_\_init\_\_.py'

I also tried to do the upgrade after removing the dipy line from the .yml  
file, but I got errors relating to PyQt  
Collecting PyQt5\>=5.10  
&nbsp;&nbsp;Using cached PyQt5-5.15.0.tar.gz (3.3 MB)  
&nbsp;&nbsp;Installing build dependencies: started  
&nbsp;&nbsp;Installing build dependencies: finished with status 'done'  
&nbsp;&nbsp;Getting requirements to build wheel: started  
&nbsp;&nbsp;Getting requirements to build wheel: finished with status 'done'  
&nbsp;&nbsp;&nbsp;&nbsp;Preparing wheel metadata: started  
&nbsp;&nbsp;&nbsp;&nbsp;Preparing wheel metadata: finished with status 'error'

I may have more details on the error tomorrow. I lost my connection to the  
remote server I'm working on.

Thanks,  
Megan  
MEG Technician  
The Mind Research Network  
1101 Yale Blvd. NE  
Albuquerque, New Mexico 87106

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**Post date:** [September 3, 2020, 7:17am UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/5 "2020-09-03T07:17:55Z")

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hi Megan,

you should ask this question to the dipy developpers. We are just users here.

Alex

---

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**Post date:** [September 3, 2020, 9:03am UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/6 "2020-09-03T09:03:08Z")

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Hi Josh,

I have not checked the function for MNE. but the original function form Guido Nolte uses FFT, and then takes the desired frequency bins. If the segments are very short (i.e. time domain multiplied by a very short rectangular window), then we know that at the frequency domain the frequency representation of the signal is convoluted by a sinc function, which makes the frequency representation not so perfect! A solution to alleviate this problem is to multiply the segments by a window shape like hanning, or others.

I suggest you to first check inside the respective functionin MNE, check how it is done there.

Best,  
Mina

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**Post date:** [September 3, 2020, 9:21pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/7 "2020-09-03T21:21:47Z")

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Hi all,  
Ok, I've asked the dipy people about that error, but I could still use help  
with the update.  
Should install instructions work for update, too? Should I just use pip to  
update mne instead of trying to use the new environment file?

I took the dipy line out of the environment file. Here is the error I'm  
getting from PyQt5....  
Any ideas/suggestions?  
Thank you,  
Megan

Collecting PyQt5\>=5.10  
&nbsp;&nbsp;Using cached PyQt5-5.15.0.tar.gz (3.3 MB)  
&nbsp;&nbsp;Installing build dependencies: started  
&nbsp;&nbsp;Installing build dependencies: finished with status 'done'  
&nbsp;&nbsp;Getting requirements to build wheel: started  
&nbsp;&nbsp;Getting requirements to build wheel: finished with status 'done'  
&nbsp;&nbsp;&nbsp;&nbsp;Preparing wheel metadata: started  
&nbsp;&nbsp;&nbsp;&nbsp;Preparing wheel metadata: finished with status 'error'  
&nbsp;&nbsp;&nbsp;&nbsp;ERROR: Command errored out with exit status 1:  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;command:  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/bin/python  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/\_vendor/pep517/\_in\_process.py  
prepare\_metadata\_for\_build\_wheel /tmp/tmperieq8r7  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;cwd: /tmp/pip-install-ci617d3e/pyqt5  
&nbsp;&nbsp;&nbsp;&nbsp;Complete output (35 lines):  
&nbsp;&nbsp;&nbsp;&nbsp;Querying qmake about your Qt installation...

/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/bin/qmake  
-query  
&nbsp;&nbsp;&nbsp;&nbsp;Traceback (most recent call last):  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/\_vendor/pep517/\_in\_process.py",  
line 126, in prepare\_metadata\_for\_build\_wheel  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;hook = backend.prepare\_metadata\_for\_build\_wheel  
&nbsp;&nbsp;&nbsp;&nbsp;AttributeError: module 'sipbuild.api' has no attribute  
'prepare\_metadata\_for\_build\_wheel'

&nbsp;&nbsp;&nbsp;&nbsp;During handling of the above exception, another exception occurred:

&nbsp;&nbsp;&nbsp;&nbsp;Traceback (most recent call last):  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/\_vendor/pep517/\_in\_process.py",  
line 280, in \<module\>  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;main()  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/\_vendor/pep517/\_in\_process.py",  
line 263, in main  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;json\_out['return\_val'] = hook(\*\*hook\_input['kwargs'])  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/\_vendor/pep517/\_in\_process.py",  
line 130, in prepare\_metadata\_for\_build\_wheel  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;return \_get\_wheel\_metadata\_from\_wheel(backend, metadata\_directory,  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/\_vendor/pep517/\_in\_process.py",  
line 159, in \_get\_wheel\_metadata\_from\_wheel  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;whl\_basename = backend.build\_wheel(metadata\_directory,  
config\_settings)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/api.py",  
line 51, in build\_wheel  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;project = AbstractProject.bootstrap('pep517')  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/abstract\_project.py",  
line 82, in bootstrap  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;project.setup(pyproject, tool, tool\_description)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/project.py",  
line 479, in setup  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;self.apply\_user\_defaults(tool)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File "project.py", line 62, in apply\_user\_defaults  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;super().apply\_user\_defaults(tool)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/pyqtbuild/project.py",  
line 89, in apply\_user\_defaults  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;super().apply\_user\_defaults(tool)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/project.py",  
line 225, in apply\_user\_defaults  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;self.builder.apply\_user\_defaults(tool)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py",  
line 77, in apply\_user\_defaults  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;self.\_get\_qt\_configuration()  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py",  
line 450, in \_get\_qt\_configuration  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;raise UserException(  
&nbsp;&nbsp;&nbsp;&nbsp;sipbuild.exceptions.UserException

---

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [September 3, 2020, 9:35pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/8 "2020-09-03T21:35:36Z")

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Building PyQt5 from source shouldn't happen. What platform are you on?  
Windows/Linux/macOS should in principle all work. Maybe you need to `pip  
install --upgrade pip`?

Can you also try:

$ python -c "import setuptools; print(setuptools.\_\_version\_\_)"

Setuptools 50.0 has broken things in SciPy lately, it's possible there are  
other bugs. If it's 50.0, try `pip install "setuptools\<50.0"`.

Eric

---

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**Post date:** [September 3, 2020, 10:05pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/9 "2020-09-03T22:05:03Z")

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Hi Eric,  
Thanks for the questions. See terminal commands and outputs below. I'm on  
Linux.  
Since pip is listed in the environment.yml file, it should have been  
upgraded by the conda env -update command, right?  
In the environment I'm trying to update, mne is broken, so I can't use  
the python -c "import mne; mne.sys\_info()" command. The results below are  
from the environment where I have a working mne 0.15 package, but I'm not  
sure which other modules have been updated there.

Thanks again,  
Megan

\*updated environment:\*  
pip --version  
pip 20.2.2 from  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip  
(python 3.8)

python -c "import setuptools; print(setuptools.\_\_version\_\_)"  
49.6.0.post20200814  
\*/updated environment\*

\*old environment:\*  
conda --version && python --version  
conda 4.3.30  
Python 3.5.4 :: Anaconda 2.5.0 (64-bit)

python -c "import mne; mne.sys\_info()"  
Platform: Linux-2.6.32-573.7.1.el6.x86\_64-x86\_64-with-centos-6.7-Final  
Python: 3.5.4 |Anaconda 2.5.0 (64-bit)| (default, Aug 14 2017,  
13:26:58) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]  
Executable:  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/bin/python  
CPU: x86\_64: 24 cores  
Memory: 126.0 GB

mne: 0.15.2  
numpy: 1.10.4 {lapack=SCIPY\_MKL\_H, blas=SCIPY\_MKL\_H}  
scipy: 0.17.0  
matplotlib: 3.0.3

sklearn: 0.17.1  
nibabel: 2.3.3  
mayavi: Not found  
pycuda: Not found  
skcuda: Not found  
pandas: 0.17.1  
\*/old environment\*

---

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [September 3, 2020, 10:15pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/10 "2020-09-03T22:15:41Z")

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If faced with this, I'd recommend creating a \*new\* conda environment rather than trying to update an old one. If it works cleanly, it's possible to delete the old one and rename the new one later if desired. The only reason I can think of \*not\* to do it this way is if your disk space is highly constrained, or if your MNE-Python environment has a lot of extra packages added that aren't in our environment.yml file (in which case it might be a bit annoying to have to manually re-install those afterward).

-- dan  
Daniel McCloy  
[https://dan.mccloy.info](https://dan.mccloy.info)  
Research Scientist  
Institute for Learning and Brain Sciences  
University of Washington

??? Original Message ???

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**Post date:** [September 3, 2020, 11:33pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/11 "2020-09-03T23:33:08Z")

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Hi Dan,  
I tried creating a new environment, and I'm still getting the dipy error.  
I'll try again removing the dipy line...  
Thanks,  
Megan

conda env create --name mne --file environment.yml  
Using Anaconda Cloud api site [https://api.anaconda.org](https://api.anaconda.org)  
Fetching package metadata ...........  
Solving package specifications: .  
pyzmq-19.0.1-p 100%

> #######################################################################################################|

Time: 0:00:00 2.75 MB/s  
jedi-0.17.2-py 100%

> #######################################################################################################|

Time: 0:00:00 7.84 MB/s  
ERROR: Invalid requirement: 'dipy --only-binary dipy'

CondaValueError: pip returned an error.

MEG Technician  
The Mind Research Network  
1101 Yale Blvd. NE  
Albuquerque, New Mexico 87106

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**Post date:** [September 4, 2020, 8:36pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/12 "2020-09-04T20:36:04Z")

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Hi all,  
I am getting the same PyQt5 error when I try the install via create  
environment.  
So attempting to creating a new environment did nothing to solve either of  
the errors I was getting trying to update the environment.  
In the new environment, I can import the mne module, but it doesn't have a  
.\_\_version\_\_ attribute or a .sysinfo() attribute, so it's still broken.

I also heard back from the dipy devs that the environment line for dipy is  
wrong. They suggest either drop either the first or second 'dipy', see  
their response below... Has anyone had success using the environment.yml  
file on the mne install page with the dipy dependency as written? I guess  
I'll also try to check with the PyQt5 devs to see about the error I'm  
getting on that.

Thanks for any help,  
Megan

PyQt5 error...  
Collecting PyQt5\>=5.10  
&nbsp;&nbsp;Using cached PyQt5-5.15.0.tar.gz (3.3 MB)  
&nbsp;&nbsp;Installing build dependencies: started  
&nbsp;&nbsp;Installing build dependencies: finished with status 'done'  
&nbsp;&nbsp;Getting requirements to build wheel: started  
&nbsp;&nbsp;Getting requirements to build wheel: finished with status 'done'  
&nbsp;&nbsp;&nbsp;&nbsp;Preparing wheel metadata: started  
&nbsp;&nbsp;&nbsp;&nbsp;Preparing wheel metadata: finished with status 'error'  
&nbsp;&nbsp;&nbsp;&nbsp;ERROR: Command errored out with exit status 1:  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;command:  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/bin/python  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/\_vendor/pep517/\_in\_process.py  
prepare\_metadata\_for\_build\_wheel /tmp/tmpdqxe1zsu  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;cwd: /tmp/pip-install-02yoibkc/pyqt5  
&nbsp;&nbsp;&nbsp;&nbsp;Complete output (35 lines):  
&nbsp;&nbsp;&nbsp;&nbsp;Querying qmake about your Qt installation...

/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/bin/qmake  
-query  
&nbsp;&nbsp;&nbsp;&nbsp;Traceback (most recent call last):  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/\_vendor/pep517/\_in\_process.py",  
line 126, in prepare\_metadata\_for\_build\_wheel  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;hook = backend.prepare\_metadata\_for\_build\_wheel  
&nbsp;&nbsp;&nbsp;&nbsp;AttributeError: module 'sipbuild.api' has no attribute  
'prepare\_metadata\_for\_build\_wheel'

&nbsp;&nbsp;&nbsp;&nbsp;During handling of the above exception, another exception occurred:

&nbsp;&nbsp;&nbsp;&nbsp;Traceback (most recent call last):  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/\_vendor/pep517/\_in\_process.py",  
line 280, in \<module\>  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;main()  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/\_vendor/pep517/\_in\_process.py",  
line 263, in main  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;json\_out['return\_val'] = hook(\*\*hook\_input['kwargs'])  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/\_vendor/pep517/\_in\_process.py",  
line 130, in prepare\_metadata\_for\_build\_wheel  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;return \_get\_wheel\_metadata\_from\_wheel(backend, metadata\_directory,  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/\_vendor/pep517/\_in\_process.py",  
line 159, in \_get\_wheel\_metadata\_from\_wheel  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;whl\_basename = backend.build\_wheel(metadata\_directory,  
config\_settings)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/api.py",  
line 51, in build\_wheel  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;project = AbstractProject.bootstrap('pep517')  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/abstract\_project.py",  
line 82, in bootstrap  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;project.setup(pyproject, tool, tool\_description)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/project.py",  
line 479, in setup  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;self.apply\_user\_defaults(tool)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File "project.py", line 62, in apply\_user\_defaults  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;super().apply\_user\_defaults(tool)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/pyqtbuild/project.py",  
line 89, in apply\_user\_defaults  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;super().apply\_user\_defaults(tool)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/project.py",  
line 225, in apply\_user\_defaults  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;self.builder.apply\_user\_defaults(tool)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py",  
line 77, in apply\_user\_defaults  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;self.\_get\_qt\_configuration()  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;File  
"/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py",  
line 450, in \_get\_qt\_configuration  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;raise UserException(  
&nbsp;&nbsp;&nbsp;&nbsp;sipbuild.exceptions.UserException

---

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [September 4, 2020, 11:43pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/13 "2020-09-04T23:43:58Z")

</div>

External Email - Use Caution

Hi all,  
The PyQt5 list helped me track down that error a bit more. The wheel build  
for PyQt5 depends on something called manylinux2014, which depends on  
CentOS7. The server I'm trying to use is CentOS 6.7.

It sounds like my environment/pip dipy issue is related to the anaconda  
version I have (may also be why mne was broken when I tried to create the  
environment).  
There are issues with the environment file using pip in older anaconda  
versions \<[Issues · conda/conda · GitHub](https://github.com/conda/conda/issues/8404&gt;%5C).  
However, this is after I do "conda update --all" in my mne environment.  
I'm having trouble figuring out how to get a newer anaconda package. The  
mne install page suggests conda version 4.6.2. It looks like I have  
4.3.30. The github issue page says the pip options issue is fixed with  
4.6.9  
Sorry to ask a conda question here, but when I try "conda update anaconda"  
I get an error saying "PackageNotInstalledError: Package is not installed  
in prefix." From searching, it sounds like I need to update my base/root  
anaconda environment, but I'm not sure I want to do that?

Also, FWIW I was able to get dipy to install using "pip install dipy  
--only-binary dipy", which sort of led me down the rabbit hole of why my  
environment didn't seem to be working with the pip options... I was also  
able to install mne using pip.

Just thought I'd update. It seems it is an issue with my system, not with  
your environment file.  
Thanks,  
Megan

conda info  
Current conda install:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;platform : linux-64  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;conda version : 4.3.30  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;conda is private : False  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;conda-env version : 4.3.30  
&nbsp;&nbsp;&nbsp;&nbsp;conda-build version : 1.19.0  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;python version : 3.5.4.final.0  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;requests version : 2.12.4  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;root environment :  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3  
(writable)  
&nbsp;&nbsp;&nbsp;&nbsp;default environment :  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;envs directories :  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;/na/homes/mschendel/.conda/envs  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;package cache :  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/pkgs  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;/na/homes/mschendel/.conda/pkgs  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;channel URLs : [main/linux-64](https://repo.continuum.io/pkgs/main/linux-64)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[main/noarch](https://repo.continuum.io/pkgs/main/noarch)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[Anaconda packages for Linux x86\_64 (64-bit)](https://repo.continuum.io/pkgs/free/linux-64)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[Anaconda packages (noarch)](https://repo.continuum.io/pkgs/free/noarch)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[r/linux-64](https://repo.continuum.io/pkgs/r/linux-64)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[r/noarch](https://repo.continuum.io/pkgs/r/noarch)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[Anaconda extras for Linux x86\_64 (64-bit)](https://repo.continuum.io/pkgs/pro/linux-64)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[Anaconda extras (noarch)](https://repo.continuum.io/pkgs/pro/noarch)  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;config file : None  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;netrc file : None  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;offline mode : False  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;user-agent : conda/4.3.30 requests/2.12.4 CPython/3.5.4  
Linux/2.6.32-573.7.1.el6.x86\_64 CentOS/6.7 glibc/2.12  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;UID:GID : 10263:8000

I was able to get dipy to install...

(mne) [mschendel at earth python]$ pip --version  
pip 20.2.2 from  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip  
(python 3.8)

(mne) [mschendel at earth envs]$ pip install dipy --only-binary dipy  
Collecting dipy  
&nbsp;&nbsp;Using cached dipy-1.1.1-cp38-cp38-manylinux1\_x86\_64.whl (8.0 MB)  
Collecting nibabel\>=3.0.0  
&nbsp;&nbsp;Using cached nibabel-3.1.1-py3-none-any.whl (3.3 MB)  
Requirement already satisfied: scipy\>=1.0 in  
./mne/lib/python3.8/site-packages (from dipy) (1.5.2)  
Requirement already satisfied: h5py\>=2.4.0 in  
./mne/lib/python3.8/site-packages (from dipy) (2.10.0)  
Requirement already satisfied: numpy\>=1.13 in  
./mne/lib/python3.8/site-packages (from nibabel\>=3.0.0-\>dipy) (1.19.1)  
Requirement already satisfied: packaging\>=14.3 in  
./mne/lib/python3.8/site-packages (from nibabel\>=3.0.0-\>dipy) (20.4)  
Requirement already satisfied: six in ./mne/lib/python3.8/site-packages  
(from h5py\>=2.4.0-\>dipy) (1.15.0)  
Requirement already satisfied: pyparsing\>=2.0.2 in  
./mne/lib/python3.8/site-packages (from

> =14.3-\>nibabel\>=3.0.0-\>dipy) (2.4.7)

Installing collected packages: nibabel, dipy  
Successfully installed dipy-1.1.1 nibabel-3.1.1

Here's where I am now:  
mne.sys\_info()  
Platform: Linux-2.6.32-573.7.1.el6.x86\_64-x86\_64-with-glibc2.10  
Python: 3.8.5 (default, Sep 4 2020, 07:30:14) [GCC 7.3.0]  
Executable:  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/bin/python3  
CPU: x86\_64: 24 cores  
Memory: 126.0 GB

mne: 0.20.8  
numpy: 1.19.1 {blas=mkl\_rt, lapack=mkl\_rt}  
scipy: 1.5.2  
matplotlib: 3.3.1 {backend=agg}

sklearn: 0.23.2  
numba: 0.50.1  
nibabel: 3.1.1  
cupy: Not found  
pandas: 1.1.1  
dipy: 1.1.1  
mayavi: Not found  
pyvista: Not found  
vtk: Not found

MEG Technician  
The Mind Research Network  
1101 Yale Blvd. NE  
Albuquerque, New Mexico 87106

---

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [September 5, 2020, 11:51am UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/14 "2020-09-05T11:51:33Z")

</div>

External Email - Use Caution

hi Megan,

thanks for the details. Unfortunately it's going to be really hard to  
debug for us  
without accessing your system. Note however that you can still use mne-python  
with just numpy, scipy and matplotlib. It will cover 90% of what you can do with  
mne-python. What you will not have is 3D support but if it's remove compute  
cluster maybe it's not a real issue.

Alex

---

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [September 5, 2020, 5:00pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/15 "2020-09-05T17:00:19Z")

</div>

External Email - Use Caution

I would just remove the `dipy` line from the environment file to see if  
that will install properly. If it doesn't, you could iteratively remove  
requirements or as Alex says, try just installing numpy, scipy, matplotlib,  
and mne.

FYI CentOS 6 reaches end-of-life for even security updates in November, so  
it might not be a bad time to consider upgrading. (Of course this is not  
the easiest solution, though!)

Eric

---

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [September 8, 2020, 10:01pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/16 "2020-09-08T22:01:55Z")

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External Email - Use Caution

Hi Alexandre, Eric,  
Thanks for the responses.  
I will see what I can accomplish without the offending packages (I got dipy  
to install, but no luck with PyQt yet). I was trying to help a  
colleague with the Visualize Source Time Courses tutorial, so we'll see  
what errors we run into.  
I found an anaconda user group, so I will ask them about why I cannot seem  
to update my conda version.

Thanks again,  
Megan

MEG Technician  
The Mind Research Network  
1101 Yale Blvd. NE  
Albuquerque, New Mexico 87106

---

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [September 10, 2020, 10:04pm UTC](https://mne.discourse.group/t/psi-frequency-bands-and-edge-artifacts/2308/17 "2020-09-10T22:04:09Z")

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Hi all,  
I managed to install a new anaconda package.  
I tried modifying the environment file to leave off dipy and PyQt, but I  
discovered I also can't install pyvistaqt. I actually was able to include  
dipy once I got the updated conda.

However, now I'm getting an error using mne.sys\_info(), and I can't use  
that command over a terminal without X11 forwarding (I am working remotely,  
so sometimes it's nice to just work on the python terminal and not get  
slowed down with the graphics forwarding). Not a deal breaker, though.

From what I can tell from the mne.sys\_info, it looks like some form of pyqt  
installed

conda --version && python --version  
conda 4.8.4  
Python 3.8.5

I created an environment from everything in the environment file under  
dependencies and with just mne for pip. Then I iteratively updated the  
environment, adding one line to the list of pip installs from the  
environment file at a time. I got some errors with pyvistaqt and PyQt.

Just terminal:  
mne.sys\_info()  
QStandardPaths: XDG\_RUNTIME\_DIR not set, defaulting to  
'/tmp/runtime-mschendel'  
qt.qpa.screen: QXcbConnection: Could not connect to display  
Could not connect to any X display.

(ipython3 quits)

Using python over a vnc with X11 forwarding enabled...  
mne.sys\_info()  
QStandardPaths: XDG\_RUNTIME\_DIR not set, defaulting to  
'/tmp/runtime-mschendel'  
Platform: Linux-2.6.32-573.7.1.el6.x86\_64-x86\_64-with-glibc2.10  
Python: 3.8.5 (default, Sep 4 2020, 07:30:14) [GCC 7.3.0]  
Executable:  
/export/research/analysis/human/jstephen/shared/programs/python/anaconda\_072020/new/envs/mne20/bin/python  
CPU: x86\_64: 24 cores  
Memory: 126.0 GB

mne: 0.20.8  
numpy: 1.19.1 {blas=mkl\_rt, lapack=mkl\_rt}  
scipy: 1.5.2  
matplotlib: 3.3.1 {backend=Qt5Agg}

sklearn: Not found  
numba: 0.50.1  
nibabel: 3.1.1  
cupy: Not found  
pandas: 1.1.1  
dipy: 1.1.1  
mayavi: 4.7.2 {qt\_api=pyqt5, PyQt5=5.9.2}  
pyvista: 0.26.0  
vtk: 9.0.1

I also tried to create an environment without pyvistaqt and PyQt.  
mne.sys\_info() looks identical  
Successfully installed PySurfer-0.11.0 appdirs-1.4.4 apptools-4.5.0  
configobj-5.0.6 dipy-1.1.1 envisage-4.9.2 imageio-ffmpeg-0.4.2 mayavi-4.7.2  
meshio-4.2.0 mne-0.20.8 neo-0.8.0 nibabel-3.1.1 nilearn-0.6.2  
python-picard-0.4 pyvista-0.26.0 quantities-0.12.4 scooby-0.5.6 sklearn-0.0  
vtk-9.0.1

Megan  
MEG Technician  
The Mind Research Network  
1101 Yale Blvd. NE  
Albuquerque, New Mexico 87106