[Mne_analysis] Mne_analysis Digest, Vol 81, Issue 9

Baptiste Gauthier gauthierb.ens at gmail.com
Thu Oct 2 04:11:34 EDT 2014
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Thanks you for all the answers and precisions,

I'm going to follow Denis' suggestions and try to use baseline data as
material for computing covariance matrices, as it ensure hat all treatments
applied to the data are also applied to baseline. As my baseline is only
200ms, i'm going to try regularization. For the particulary artifacted
subjects, I'm going to re-examine carefully the raw data, as I could have
forgot or misrecord bad channels.

Just one last question: what is the gain of combining all sensor types
(grads, mags, eeg) ? Here I know from visual inspection and sensor-level
analysis that my eeg data is noisier than meg ...

thanks again!

Baptiste


2014-10-02 8:54 GMT+02:00 <mne_analysis-request at nmr.mgh.harvard.edu>:

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> Today's Topics:
>
>    1. Re: What is a "good" noise covariance matrix? (Ghuman, Avniel)
>    2. Re: python-MNE installation (raij at nmr.mgh.harvard.edu)
>    3. Re: python-MNE installation (Alexandre Gramfort)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 1 Oct 2014 21:42:57 +0000
> From: "Ghuman, Avniel" <ghumana at upmc.edu>
> Subject: Re: [Mne_analysis] What is a "good" noise covariance matrix?
> To: Discussion and support forum for the users of MNE Software
>         <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID: <D051EC23.7B7DD%ghumana at upmc.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Dan,
>
> Agreed Dan, though that has to be balanced against potential
> interpretability issues with regards to having multiple inverse operators.
> Specifically, if one wants to compare across frequency bands of interest,
> but the source maps for those bands were made with different inverse
> operators (e.g. the data at the same source location comes from different
> sensor configurations at different frequencies), the interpretation of
> those results becomes difficult.
>
> Best wishes,
> Avniel
>
> On 10/1/14 2:20 PM, "dgw" <dgwakeman at gmail.com> wrote:
>
> >That and other "Unless" statements, is why I strongly recommend
> >treating all your data identically. One cannot know how good each
> >person's system and default SSPs etc. are, but if you treat all data
> >the same (which has no downside) you at least can expect the same
> >responses.
> >
> >In the plots Baptiste originally sent the "bad?" plot looked as though
> >there were artifacts in the empty room recording, which created the
> >the strikingly different plot. Examining the raw data is a must.
> >
> >HTH
> >D
> >
> >On Wed, Oct 1, 2014 at 12:00 PM, Ghuman, Avniel <ghumana at upmc.edu> wrote:
> >> Hi Hari,
> >>
> >> That is in part because the noise floor of SQUIDs are frequency
> >>dependent.
> >> However, the question is not whether the covariance matrix is biased
> >> towards being influenced by low frequencies, but whether or not the
> >> overall shape of the covariance matrix differs across frequencies.
> >>Unless
> >> you have multiple sources of environmental noise with different spatial
> >> distributions in sensor space, each of which has a different frequency
> >> dependance, there should be no effect of band pass filtering on the
> >> covariance matrix built from empty room. Hopefully though, the intrinsic
> >> SSP projections that are attached to the raw fif files would address
> >>much
> >> of that.
> >>
> >> Best wishes,
> >> Avniel
> >>
> >> On 10/1/14 11:13 AM, "Hari Bharadwaj" <hari at nmr.mgh.harvard.edu> wrote:
> >>
> >>>Whether the band pass makes a difference or not with empty room data in
> >>>my experience depends on the band that is included... The spatial
> >>>covariance appears to be dominated by he lower frequencies...
> >>>
> >>>Regardless, I can't think of any reason to not process the noise data
> >>>segments in the exact same way as the data segments of interest.
> >>>
> >>>Hari
> >>>
> >>>> On Oct 1, 2014, at 11:07 AM, "Ghuman, Avniel" <ghumana at upmc.edu>
> >>>>wrote:
> >>>>
> >>>> To answer this question:
> >>>>
> >>>> Does it make sense to band-pass the empty room signal with the same
> >>>>classical band pass applied to the data? Can it improve a bit the
> >>>>thing?
> >>>>
> >>>> My experience is that, if you are using empty room data, the band pass
> >>>>makes essentially no difference. With baseline segments it can make a
> >>>>little difference, but even here the difference is minimal between
> >>>>broadband and band passed. Definitely though, at least broad-band pass
> >>>>the empty room and/or baseline though to remove high frequency noise
> >>>>and
> >>>>very low frequency drift (1-50 Hz or 1-100 Hz or something of that
> >>>>nature) and apply any SSP projectors you use in your real data.
> >>>>
> >>>> Best wishes,
> >>>> Avniel
> >>>>
> >>>> From: Denis-Alexander Engemann
> >>>><denis.engemann at gmail.com<mailto:denis.engemann at gmail.com>>
> >>>> Reply-To: Discussion and support forum for the users of MNE Software
> >>>><mne_analysis at nmr.mgh.harvard.edu<mailto:
> mne_analysis at nmr.mgh.harvard.e
> >>>>du
> >>>>>>
> >>>> Date: Wednesday, October 1, 2014 10:31 AM
> >>>> To: Discussion and support forum for the users of MNE Software
> >>>><mne_analysis at nmr.mgh.harvard.edu<mailto:
> mne_analysis at nmr.mgh.harvard.e
> >>>>du
> >>>>>>
> >>>> Subject: Re: [Mne_analysis] What is a "good" noise covariance matrix?
> >>>>
> >>>> Hi Baptiste,
> >>>>
> >>>> If you have classical ERFs and a 'baseline' I would not rule out
> >>>>computing the noise cov from baseline segments, In my experience
> >>>>inverse
> >>>>solutions based on such a 'subject' noise covariance are often more
> >>>>focal. I had cases where analyses would have failed using an empty room
> >>>>noise cov.
> >>>> I share your intuition about the classification of the noise
> >>>>covariances you have sent.
> >>>> Very roughly you can say that a covariance is better if its matrix
> >>>>plot
> >>>>looks more diagonal.
> >>>> As the covariance is used for whitening the data (sensor data + lead
> >>>>field) you can investigate its quality by computing a whitener and
> >>>>applying it to the data:
> >>>>
> >>>>
> >>>>
> http://martinos.org/mne/stable/auto_examples/plot_evoked_whitening.html
> >>>>
> >>>> If the majority of signals in the baseline (assumed to represent
> >>>>signals of non-interest) are not within -1.96 and 1.96 something is
> >>>>wrong. The cov is actually good if the covariance matrix of the
> >>>>whitened
> >>>>signals looks like an identity matrix.
> >>>>
> >>>> Regularization is important when the number of samples used to compute
> >>>>the noise cov is small.
> >>>> But it's also important combine different sensort types.
> >>>>
> >>>> C.f.
> >>>>
> http://martinos.org/mne/stable/auto_examples/inverse/plot_make_inverse_
> >>>>op
> >>>>erator.html#example-inverse-plot-make-inverse-operator-py
> >>>>
> >>>>
> >>>> HTH,
> >>>> Denis
> >>>>
> >>>> 2014-10-01 16:02 GMT+02:00 Baptiste Gauthier
> >>>><gauthierb.ens at gmail.com<mailto:gauthierb.ens at gmail.com>>:
> >>>> Dear mne-python experts and users,
> >>>>
> >>>> following the guidelines of source reconstruction of ERFs, I estimated
> >>>>noise covariance matrices from empty room noise (neuromag system) for
> >>>>calculating inverse operator. When looking at the source estimates I
> >>>>got, it appears that source amplitude can be very variable, not in term
> >>>>of timecourse patterns (which is good for ERFs) but in term of absolute
> >>>>amplitude (need to play with "fmult" in mne_analyze visualization
> >>>>tools;
> >>>>I suppose it's bad for stats).
> >>>> So I checked if the noise estimation was similar across subjects and
> >>>>realize I have no criterion to decide if noise covariance was "ok" or
> >>>>not...
> >>>> What criterion should I apply?
> >>>> Should I use then regularization for "bad" subjects?
> >>>>
> >>>> PS:find attached several noise covariance matrices from my study
> >>>> PPS: Does it make sense to band-pass the empty room signal with the
> >>>>same classical band pass applied to the data? Can it improve a bit the
> >>>>thing?
> >>>>
> >>>> Best,
> >>>>
> >>>> Baptiste Gauthier
> >>>>
> >>>>
> >>>>
> >>>> [https://ssl.gstatic.com/docs/doclist/images/icon_11_image_list.png]
> >>>>bad?.png<
> https://docs.google.com/file/d/0B_eZxstAMJQscGpiOF9VY00yLWc/ed
> >>>>it
> >>>>?usp=drive_web>
> >>>>
> >>>> [https://ssl.gstatic.com/docs/doclist/images/icon_11_image_list.png]
> >>>>good?.png<
> https://docs.google.com/file/d/0B_eZxstAMJQsY01WdGlJbENHa0U/e
> >>>>di
> >>>>t?usp=drive_web>
> >>>>
> >>>>
> >>>> 2014-10-01 14:05 GMT+02:00 Baptiste Gauthier
> >>>><gauthierb.ens at gmail.com<mailto:gauthierb.ens at gmail.com>>:
> >>>> Dear mne-python experts and users,
> >>>>
> >>>> following the guidelines of source reconstruction of ERFs, I estimated
> >>>>noise covariance matrices from empty room noise (neuromag system) for
> >>>>calculating inverse operator. When looking at the source estimates I
> >>>>got, it appears that source amplitude can be very variable, not in term
> >>>>of timecourse patterns (which is good for ERFs) but in term of absolute
> >>>>amplitude (need to play with "fmult" in mne_analyze visualization
> >>>>tools;
> >>>>I suppose it's bad for stats).
> >>>> So I checked if the noise estimation was similar across subjects and
> >>>>realize I have no criterion to decide if noise covariance was "ok" or
> >>>>not...
> >>>> What criterion should I apply?
> >>>> Should I use then regularization for "bad" subjects?
> >>>>
> >>>> PS:find attached several noise covariance matrices from my study
> >>>> PPS: Does it make sense to band-pass the empty room signal with the
> >>>>same classical band pass applied to the data? Can it improve a bit the
> >>>>thing?
> >>>>
> >>>> Best,
> >>>>
> >>>> Baptiste Gauthier
> >>>>
> >>>> --
> >>>> Baptiste Gauthier
> >>>> Postdoctoral Research Fellow
> >>>>
> >>>> INSERM-CEA Cognitive Neuroimaging unit
> >>>> CEA/SAC/DSV/DRM/Neurospin center
> >>>> B?t 145, Point Courier 156
> >>>> F-91191 Gif-sur-Yvette Cedex FRANCE
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Baptiste Gauthier
> >>>> Postdoctoral Research Fellow
> >>>>
> >>>> INSERM-CEA Cognitive Neuroimaging unit
> >>>> CEA/SAC/DSV/DRM/Neurospin center
> >>>> B?t 145, Point Courier 156
> >>>> F-91191 Gif-sur-Yvette Cedex FRANCE
> >>>>
> >>>> _______________________________________________
> >>>> Mne_analysis mailing list
> >>>>
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> Mne_analysis at nmr.mgh.harvard.ed
> >>>>u>
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> >>>>
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>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 1 Oct 2014 20:01:59 -0400 (EDT)
> From: raij at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] python-MNE installation
> To: "Discussion and support forum for the users of MNE Software"
>         <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
>         <
> 40973.165.124.149.103.1412208119.squirrel at mail.nmr.mgh.harvard.edu>
> Content-Type: text/plain;charset=iso-8859-1
>
>
> Hi Alex,
>
> I think this is a path error at multiple levels - installations go one way
> and the expected paths in another. I tried to follow your suggestions
> (uninstall yum pip > install canopy pip > re-install MNE python) but keep
> getting similar/same errors as before. Some observations and questions
> (details of terminal commands and feedback at the end):
>
> 1. Do I need to cd to a specific directory when I do "easy_install pip" and
> "pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev?"
> This seems to determine where the "src" dir and paths are set (I did not
> see this mentioned in the "getting started" web page - and now after
> several installation attempts I see I have a few "src" dirs in different
> locations).
>
> 2. For cleaning up extra copies (see above), how do I remove spurious mne
> python installations? Attempt to "pip uninstall mne-python" at the dirs
> where they were installed gives the error:
> Cannot uninstall requirement mne-python, not installed
> Storing debug log for failure in /root/.pip/pip.log
>
> 3. Post installation, where should the user level ~/.cshrc path point? I
> now have it at
> setenv PATH /usr/pubsw/packages/python/System/bin:${PATH}
>
> 4. As one might reasonable expect given the above mess, the good old
> errors remain: given from a csh window either as root or as a user, the
> command "ipython --pylab qt", and ipython followed by ">>>import mne"
> result in the same errors as before.
>
> Cheers,
>
> Tommi
>
>
> DETAILS:
>
> su root + pw
> csh
> whoami: root
>
> - uninstall yum-pip <yum remove python-pip> as root. Result: OK
>
> - install Canopy pip <easy_install pip> as root. Result: OK. Details:
> [raij at tmsh raij]# easy_install pip
> Searching for pip
> Reading http://pypi.python.org/simple/pip/
> Best match: pip 1.5.6
> Downloading
>
> https://pypi.python.org/packages/source/p/pip/pip-1.5.6.tar.gz#md5=01026f87978932060cc86c1dc527903e
> Processing pip-1.5.6.tar.gz
> Running pip-1.5.6/setup.py -q bdist_egg --dist-dir
> /tmp/easy_install-HjVeBr/pip-1.5.6/egg-dist-tmp-HRsylX
> warning: no files found matching 'pip/cacert.pem'
> warning: no files found matching '*.html' under directory 'docs'
> warning: no previously-included files matching '*.rst' found under
> directory 'docs/_build'
> no previously-included directories found matching 'docs/_build/_sources'
> Adding pip 1.5.6 to easy-install.pth file
> Installing pip script to /usr/bin
> Installing pip2.6 script to /usr/bin
> Installing pip2 script to /usr/bin
> Installed /usr/lib/python2.6/site-packages/pip-1.5.6-py2.6.egg
> Processing dependencies for pip
> Finished processing dependencies for pip
>
> - re-install MNE-python <pip install -e
> git+https://github.com/mne-tools/mne-python#egg=mne-dev> as root. Result
> looks OK but for some reason setup.py path points to my home dir even
> though I am here as root:
>
> [raij at tmsh raij]# pip install -e
> git+https://github.com/mne-tools/mne-python#egg=mne-dev
> Obtaining mne from git+https://github.com/mne-tools/mne-python#egg=mne-dev
>   Cloning https://github.com/mne-tools/mne-python to ./src/mne
>   Running setup.py (path:/home/raij/src/mne/setup.py) egg_info for package
> mne
>     build_src
>     warning: no previously-included files matching '*' found under
> directory 'examples/MNE-sample-data'
>   Installing extra requirements: 'egg'
> Installing collected packages: mne
>   Running setup.py develop for mne
>     changing mode of build/scripts.linux-x86_64-2.6/mne from 644 to 755
>     build_src
>     warning: no previously-included files matching '*' found under
> directory 'examples/MNE-sample-data'
>     Creating /usr/lib/python2.6/site-packages/mne.egg-link (link to .)
>     Removing mne 0.9.git from easy-install.pth file
>     Adding mne 0.9.git to easy-install.pth file
>     Installing mne script to /usr/bin
>
>     Installed /home/raij/src/mne
> Successfully installed mne
> Cleaning up...
>
>
> > hi Tommi,
> >
> >> Then, I checked that both "which python" and "which pip" already point
> >> to
> >> Canopy (I did not do anything to the system yet). Specifically:
> >> which python
> >> /usr/pubsw/packages/python/System/bin/python
> >> which pip
> >> /usr/pubsw/packages/python/System/bin/pip
> >
> > good
> >
> >> Next, I re-installed (as root) the python mne package just to make sure
> >> it
> >> is there:
> >> pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev
> >
> > what did it say? did it complete successfully?
> >
> > if pip is from canopy and you see no error then typing in (i)python
> >
> > import mne
> >
> > should really work.
> >
> >> However, the errors for
> >> ipython --pylab gt
> >> and
> >> ipython -> import mne
> >>
> >> remain exactly the same as before.
> >>
> >> If you still believe I need to uninstall the pip I installed with yum, I
> >> would greatly appreciate if you could let me know which command I should
> >> use for uninstallation (I found a ton of different ways, and some of
> >> these
> >> will likely mess up the system in more than one way).
> >
> > yum uninstall python-pip
> >
> > ?
> >
> > don't hesitate to paste error messages.
> >
> > Alex
> >
> > PS : we're going to improve the getting started doc...
> > PS2 : if you really struggle get rid of canopy and give a try to
> > anaconda installing it in your home folder without root access.
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> >
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 2 Oct 2014 08:54:06 +0200
> From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
> Subject: Re: [Mne_analysis] python-MNE installation
> To: Discussion and support forum for the users of MNE Software
>         <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
>         <CADeotZpP4Mo=
> 1V0G4Xyc1UQWioryUfTioctk7sqY_mVLZo9OFw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> hi Tommi,
>
> > 1. Do I need to cd to a specific directory when I do "easy_install pip"
> and
> > "pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev
> ?"
> > This seems to determine where the "src" dir and paths are set (I did not
> > see this mentioned in the "getting started" web page - and now after
> > several installation attempts I see I have a few "src" dirs in different
> > locations).
>
> no you can be anywhere
>
> > 2. For cleaning up extra copies (see above), how do I remove spurious mne
> > python installations? Attempt to "pip uninstall mne-python" at the dirs
> > where they were installed gives the error:
> > Cannot uninstall requirement mne-python, not installed
> > Storing debug log for failure in /root/.pip/pip.log
>
> use "pip uninstall mne"
>
> "mne" is the name on pypi.
>
> > 3. Post installation, where should the user level ~/.cshrc path point? I
> > now have it at
> > setenv PATH /usr/pubsw/packages/python/System/bin:${PATH}
>
> yes I think.
>
> > DETAILS:
> >
> > su root + pw
> > csh
> > whoami: root
> >
> > - uninstall yum-pip <yum remove python-pip> as root. Result: OK
>
> good
>
> > - install Canopy pip <easy_install pip> as root. Result: OK. Details:
> > [raij at tmsh raij]# easy_install pip
> > Searching for pip
> > Reading http://pypi.python.org/simple/pip/
> > Best match: pip 1.5.6
> > Downloading
> >
> https://pypi.python.org/packages/source/p/pip/pip-1.5.6.tar.gz#md5=01026f87978932060cc86c1dc527903e
> > Processing pip-1.5.6.tar.gz
> > Running pip-1.5.6/setup.py -q bdist_egg --dist-dir
> > /tmp/easy_install-HjVeBr/pip-1.5.6/egg-dist-tmp-HRsylX
> > warning: no files found matching 'pip/cacert.pem'
> > warning: no files found matching '*.html' under directory 'docs'
> > warning: no previously-included files matching '*.rst' found under
> > directory 'docs/_build'
> > no previously-included directories found matching 'docs/_build/_sources'
> > Adding pip 1.5.6 to easy-install.pth file
> > Installing pip script to /usr/bin
> > Installing pip2.6 script to /usr/bin
> > Installing pip2 script to /usr/bin
> > Installed /usr/lib/python2.6/site-packages/pip-1.5.6-py2.6.egg
> > Processing dependencies for pip
> > Finished processing dependencies for pip
>
> if you see /usr/lib and not /usr/pubsw/packages/python/System/...
> you install on the linux tree and not canopy. That's the problem.
> easy_install and canopy seem to install stuff in the wrong place.
> You should have everything in the canopy folder.
>
> same thing happens below with pip install mne
>
> if you did not do anywrong and easy_install is the one from canopy
> then canopy is buggy and you should give a try to anaconda.
>
> Alex
>
> > - re-install MNE-python <pip install -e
> > git+https://github.com/mne-tools/mne-python#egg=mne-dev> as root. Result
> > looks OK but for some reason setup.py path points to my home dir even
> > though I am here as root:
> >
> > [raij at tmsh raij]# pip install -e
> > git+https://github.com/mne-tools/mne-python#egg=mne-dev
> > Obtaining mne from git+
> https://github.com/mne-tools/mne-python#egg=mne-dev
> >   Cloning https://github.com/mne-tools/mne-python to ./src/mne
> >   Running setup.py (path:/home/raij/src/mne/setup.py) egg_info for
> package
> > mne
> >     build_src
> >     warning: no previously-included files matching '*' found under
> > directory 'examples/MNE-sample-data'
> >   Installing extra requirements: 'egg'
> > Installing collected packages: mne
> >   Running setup.py develop for mne
> >     changing mode of build/scripts.linux-x86_64-2.6/mne from 644 to 755
> >     build_src
> >     warning: no previously-included files matching '*' found under
> > directory 'examples/MNE-sample-data'
> >     Creating /usr/lib/python2.6/site-packages/mne.egg-link (link to .)
> >     Removing mne 0.9.git from easy-install.pth file
> >     Adding mne 0.9.git to easy-install.pth file
> >     Installing mne script to /usr/bin
> >
> >     Installed /home/raij/src/mne
> > Successfully installed mne
> > Cleaning up...
> >
> >
> >> hi Tommi,
> >>
> >>> Then, I checked that both "which python" and "which pip" already point
> >>> to
> >>> Canopy (I did not do anything to the system yet). Specifically:
> >>> which python
> >>> /usr/pubsw/packages/python/System/bin/python
> >>> which pip
> >>> /usr/pubsw/packages/python/System/bin/pip
> >>
> >> good
> >>
> >>> Next, I re-installed (as root) the python mne package just to make sure
> >>> it
> >>> is there:
> >>> pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev
> >>
> >> what did it say? did it complete successfully?
> >>
> >> if pip is from canopy and you see no error then typing in (i)python
> >>
> >> import mne
> >>
> >> should really work.
> >>
> >>> However, the errors for
> >>> ipython --pylab gt
> >>> and
> >>> ipython -> import mne
> >>>
> >>> remain exactly the same as before.
> >>>
> >>> If you still believe I need to uninstall the pip I installed with yum,
> I
> >>> would greatly appreciate if you could let me know which command I
> should
> >>> use for uninstallation (I found a ton of different ways, and some of
> >>> these
> >>> will likely mess up the system in more than one way).
> >>
> >> yum uninstall python-pip
> >>
> >> ?
> >>
> >> don't hesitate to paste error messages.
> >>
> >> Alex
> >>
> >> PS : we're going to improve the getting started doc...
> >> PS2 : if you really struggle get rid of canopy and give a try to
> >> anaconda installing it in your home folder without root access.
> >> _______________________________________________
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> >> Mne_analysis at nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >>
> >>
> >
> >
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> End of Mne_analysis Digest, Vol 81, Issue 9
> *******************************************
>



-- 
Baptiste Gauthier
Postdoctoral Research Fellow

INSERM-CEA Cognitive Neuroimaging unit
CEA/SAC/DSV/DRM/Neurospin center
Bât 145, Point Courier 156
F-91191 Gif-sur-Yvette Cedex FRANCE
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