[Mne_analysis] Mne_analysis Digest, Vol 79, Issue 43

Kambiz Tavabi ktavabi at uw.edu
Mon Aug 18 17:58:01 EDT 2014
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Thanks Martin.

The command generates an error trying to import pkg_resources. What is
this? I can't find a module pkg_resources using pip, however there seems to
be a pkg-resources. Is that what is missing?
Here is the trace:
Traceback (most recent call last):
  File "/home/kambiz/anaconda/bin/mne", line 4, in <module>
    import pkg_resources
  File
"~anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/pkg_resources.py",
line 2829, in <module>
  File
"~anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/pkg_resources.py",
line 449, in _build_master
  File
"~anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/pkg_resources.py",
line 742, in require
  File
"~anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/pkg_resources.py",
line 639, in resolve
pkg_resources.DistributionNotFound: mne==0.8.git

Kam


------------------------------------------------------------
Kambiz Tavabi PhD
Institute for Learning & Brain Sciences
1715 Columbia Road N
Portage Bay Building
Box 357988
University of Washington
Seattle, WA 98195-7988
Tel: 206-685-6173
------------------------------------------------------------


On Mon, Aug 18, 2014 at 2:31 PM, <mne_analysis-request at nmr.mgh.harvard.edu>
wrote:

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> Today's Topics:
>
>    1. Re: Mne_analysis Digest, Vol 78, Issue 20 (Martin Luessi)
>    2. Re: Mne_analysis Digest, Vol 78, Issue 20 (Mainak Jas)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 18 Aug 2014 16:59:38 -0400
> From: Martin Luessi <mluessi at nmr.mgh.harvard.edu>
> Subject: Re: [Mne_analysis] Mne_analysis Digest, Vol 78, Issue 20
> To: Discussion and support forum for the users of MNE Software
>         <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID: <53F2693A.6040808 at nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Kambiz,
>
> The report generator is part of MNE-Python, not the MNE command-line tools.
>
> Best,
>
> Martin
>
> On 08/18/14 16:52, Kambiz Tavabi wrote:
> > hi all,
> > I am using MNE-2.7.4-3439; I don't see the mne_report program in this
> > build, nor in the 3443 build.
> > Is there some other place the program is available? and if so can I get
> > my hands on it? Thanks. Kam
> >
> > ------------------------------------------------------------
> > Kambiz Tavabi PhD
> > Institute for Learning & Brain Sciences
> > 1715 Columbia Road N
> > Portage Bay Building
> > Box 357988
> > University of Washington
> > Seattle, WA 98195-7988
> > Tel: 206-685-6173
> > ------------------------------------------------------------
> >
> >
> > On Fri, Jul 11, 2014 at 11:35 AM,
> > <mne_analysis-request at nmr.mgh.harvard.edu
> > <mailto:mne_analysis-request at nmr.mgh.harvard.edu>> wrote:
> >
> >     Send Mne_analysis mailing list submissions to
> >             mne_analysis at nmr.mgh.harvard.edu
> >     <mailto:mne_analysis at nmr.mgh.harvard.edu>
> >
> >     To subscribe or unsubscribe via the World Wide Web, visit
> >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >     or, via email, send a message with subject or body 'help' to
> >             mne_analysis-request at nmr.mgh.harvard.edu
> >     <mailto:mne_analysis-request at nmr.mgh.harvard.edu>
> >
> >     You can reach the person managing the list at
> >             mne_analysis-owner at nmr.mgh.harvard.edu
> >     <mailto:mne_analysis-owner at nmr.mgh.harvard.edu>
> >
> >     When replying, please edit your Subject line so it is more specific
> >     than "Re: Contents of Mne_analysis digest..."
> >
> >
> >     Today's Topics:
> >
> >        1. mne report command (Mainak Jas)
> >        2. Re: mne report command (Alexandre Gramfort)
> >        3. Re: mne report command (Denis-Alexander Engemann)
> >        4. Re: mne report command (dgw)
> >        5. Re: mne report command (Alexandre Gramfort)
> >
> >
> >
>  ----------------------------------------------------------------------
> >
> >     Message: 1
> >     Date: Fri, 11 Jul 2014 18:56:31 +0300 (EEST)
> >     From: "Mainak Jas" <mainak at neuro.hut.fi <mailto:mainak at neuro.hut.fi
> >>
> >     Subject: [Mne_analysis] mne report command
> >     To: mne_analysis at nmr.mgh.harvard.edu
> >     <mailto:mne_analysis at nmr.mgh.harvard.edu>
> >     Message-ID: <43974.82.130.26.44.1405094191.squirrel at neuro.hut.fi
> >     <mailto:43974.82.130.26.44.1405094191.squirrel at neuro.hut.fi>>
> >     Content-Type: text/plain;charset=iso-8859-1
> >
> >     Dear all,
> >
> >     We're converging on the `mne report` command that I was working for
> the
> >     Google Summer of Code this year.
> >
> >     The idea is to run the `mne report` command as below:
> >
> >     $ mne report --path MNE-sample-data/ --subjects-dir
> >     MNE-sample-data/subjects --subject sample
> >
> >     providing it the data directory whose report must be created. It will
> >     generate a report as a single html file which can be easily shared
> with
> >     collaborators via email or dropbox. A link to the report generated
> from
> >     the MNE sample dataset is provided below:
> >
> >     https://dl.dropboxusercontent.com/u/3915954/report.html
> >
> >     The motivation is that it can be used to generate a quick
> >     summary/statistics of the results and do a quality check with minimal
> >     scripting. Typically, this is something one might want to run one day
> >     after data collection.
> >
> >     We also provide a python interface for more advanced users who want
> to
> >     embed their own custom plots in the report.
> >
> >     Any feedback towards improving this is most appreciated. Thanks!
> >
> >     Best regards,
> >     Mainak
> >
> >
> >     ------------------------------
> >
> >     Message: 2
> >     Date: Fri, 11 Jul 2014 18:27:31 +0200
> >     From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr
> >     <mailto:alexandre.gramfort at telecom-paristech.fr>>
> >     Subject: Re: [Mne_analysis] mne report command
> >     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.edu>>
> >     Message-ID:
> >
> >     <CADeotZqJvH5g1jqoUUwWKxa4FiP5M4MMOzVcTkfy9cvoFMd8Fw at mail.gmail.com
> >     <mailto:
> CADeotZqJvH5g1jqoUUwWKxa4FiP5M4MMOzVcTkfy9cvoFMd8Fw at mail.gmail.com>>
> >     Content-Type: text/plain; charset=UTF-8
> >
> >     hi,
> >
> >     I am already really happy to see what Mainak has achieved but if you
> >     think some relevant information is missing or not well highlighted,
> >     it's the moment to ask so we can make it happen for the next release.
> >
> >     Please take a minute to give some feedback and suggest improvements.
> >
> >     Cheers,
> >     Alex
> >
> >
> >     On Fri, Jul 11, 2014 at 5:56 PM, Mainak Jas <mainak at neuro.hut.fi
> >     <mailto:mainak at neuro.hut.fi>> wrote:
> >     > Dear all,
> >     >
> >     > We're converging on the `mne report` command that I was working
> >     for the
> >     > Google Summer of Code this year.
> >     >
> >     > The idea is to run the `mne report` command as below:
> >     >
> >     > $ mne report --path MNE-sample-data/ --subjects-dir
> >     > MNE-sample-data/subjects --subject sample
> >     >
> >     > providing it the data directory whose report must be created. It
> will
> >     > generate a report as a single html file which can be easily shared
> >     with
> >     > collaborators via email or dropbox. A link to the report generated
> >     from
> >     > the MNE sample dataset is provided below:
> >     >
> >     > https://dl.dropboxusercontent.com/u/3915954/report.html
> >     >
> >     > The motivation is that it can be used to generate a quick
> >     > summary/statistics of the results and do a quality check with
> minimal
> >     > scripting. Typically, this is something one might want to run one
> day
> >     > after data collection.
> >     >
> >     > We also provide a python interface for more advanced users who
> want to
> >     > embed their own custom plots in the report.
> >     >
> >     > Any feedback towards improving this is most appreciated. Thanks!
> >     >
> >     > Best regards,
> >     > Mainak
> >     > _______________________________________________
> >     > Mne_analysis mailing list
> >     > Mne_analysis at nmr.mgh.harvard.edu
> >     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >     >
> >     >
> >     > The information in this e-mail is intended only for the person to
> >     whom it is
> >     > addressed. If you believe this e-mail was sent to you in error and
> >     the e-mail
> >     > contains patient information, please contact the Partners
> >     Compliance HelpLine at
> >     > http://www.partners.org/complianceline . If the e-mail was sent to
> >     you in error
> >     > but does not contain patient information, please contact the
> >     sender and properly
> >     > dispose of the e-mail.
> >     >
> >
> >
> >     ------------------------------
> >
> >     Message: 3
> >     Date: Fri, 11 Jul 2014 18:44:28 +0200
> >     From: Denis-Alexander Engemann <denis.engemann at gmail.com
> >     <mailto:denis.engemann at gmail.com>>
> >     Subject: Re: [Mne_analysis] mne report command
> >     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.edu>>
> >     Message-ID:
> >
> >     <CA+MN3Os+TROLw22hTMcK5G3VA+3KjQw6UCsPxBNZ99ztTbaivA at mail.gmail.com
> >     <mailto:
> CA%2BMN3Os%2BTROLw22hTMcK5G3VA%2B3KjQw6UCsPxBNZ99ztTbaivA at mail.gmail.com>>
> >     Content-Type: text/plain; charset="utf-8"
> >
> >     Hi all,
> >
> >     here is an example that shows how to create a custom report:
> >
> >     https://gist.github.com/dengemann/dedbf84d07d79975d5a0
> >
> >     Best,
> >     Denis
> >
> >
> >     On Fri, Jul 11, 2014 at 6:27 PM, Alexandre Gramfort <
> >     alexandre.gramfort at telecom-paristech.fr
> >     <mailto:alexandre.gramfort at telecom-paristech.fr>> wrote:
> >
> >     > hi,
> >     >
> >     > I am already really happy to see what Mainak has achieved but if
> you
> >     > think some relevant information is missing or not well highlighted,
> >     > it's the moment to ask so we can make it happen for the next
> release.
> >     >
> >     > Please take a minute to give some feedback and suggest
> improvements.
> >     >
> >     > Cheers,
> >     > Alex
> >     >
> >     >
> >     > On Fri, Jul 11, 2014 at 5:56 PM, Mainak Jas <mainak at neuro.hut.fi
> >     <mailto:mainak at neuro.hut.fi>> wrote:
> >     > > Dear all,
> >     > >
> >     > > We're converging on the `mne report` command that I was working
> >     for the
> >     > > Google Summer of Code this year.
> >     > >
> >     > > The idea is to run the `mne report` command as below:
> >     > >
> >     > > $ mne report --path MNE-sample-data/ --subjects-dir
> >     > > MNE-sample-data/subjects --subject sample
> >     > >
> >     > > providing it the data directory whose report must be created. It
> >     will
> >     > > generate a report as a single html file which can be easily
> >     shared with
> >     > > collaborators via email or dropbox. A link to the report
> >     generated from
> >     > > the MNE sample dataset is provided below:
> >     > >
> >     > > https://dl.dropboxusercontent.com/u/3915954/report.html
> >     > >
> >     > > The motivation is that it can be used to generate a quick
> >     > > summary/statistics of the results and do a quality check with
> >     minimal
> >     > > scripting. Typically, this is something one might want to run
> >     one day
> >     > > after data collection.
> >     > >
> >     > > We also provide a python interface for more advanced users who
> >     want to
> >     > > embed their own custom plots in the report.
> >     > >
> >     > > Any feedback towards improving this is most appreciated. Thanks!
> >     > >
> >     > > Best regards,
> >     > > Mainak
> >     > > _______________________________________________
> >     > > Mne_analysis mailing list
> >     > > Mne_analysis at nmr.mgh.harvard.edu
> >     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> >     > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >     > >
> >     > >
> >     > > The information in this e-mail is intended only for the person
> >     to whom
> >     > it is
> >     > > addressed. If you believe this e-mail was sent to you in error
> >     and the
> >     > e-mail
> >     > > contains patient information, please contact the Partners
> Compliance
> >     > HelpLine at
> >     > > http://www.partners.org/complianceline . If the e-mail was sent
> >     to you
> >     > in error
> >     > > but does not contain patient information, please contact the
> >     sender and
> >     > properly
> >     > > dispose of the e-mail.
> >     > >
> >     > _______________________________________________
> >     > Mne_analysis mailing list
> >     > Mne_analysis at nmr.mgh.harvard.edu
> >     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >     >
> >     -------------- next part --------------
> >     An HTML attachment was scrubbed...
> >     URL:
> >
> http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140711/a59d133a/attachment-0001.html
> >
> >     ------------------------------
> >
> >     Message: 4
> >     Date: Fri, 11 Jul 2014 13:23:04 -0400
> >     From: dgw <dgwakeman at gmail.com <mailto:dgwakeman at gmail.com>>
> >     Subject: Re: [Mne_analysis] mne report command
> >     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.edu>>
> >     Message-ID:
> >
> >     <CADM2BTj5+c-ber6YWJ52NJvTzWS_iyt_sA-CQ94D_eMnPYMK4w at mail.gmail.com
> >     <mailto:
> CADM2BTj5%2Bc-ber6YWJ52NJvTzWS_iyt_sA-CQ94D_eMnPYMK4w at mail.gmail.com>>
> >     Content-Type: text/plain; charset=UTF-8
> >
> >     Hi Mainak,
> >
> >     This looks great!
> >
> >     My suggestions:
> >
> >     Remove the full path from the names of each file (just put the path
> at
> >     the top of the report).
> >     No space between the colon and file type:
> >     Events : MNE-sample-data/MEG/sample/ernoise_raw-eve.fif -> Events:
> >     ernoise_raw-eve.fif
> >
> >     By default don't include events with value of 0 (maybe include it as
> >     an option). In most cases these are not true events.
> >
> >     The covariance matrix scaling for gradiometers in the sample file
> >     seems flat.
> >
> >     At least an option to force a scaling factor for each file type
> >     (because it can be confusing for example that the left and right
> >     visual evoked examples have different scalings for the gradiometers).
> >
> >     It would be most helpful to split the Trans plot into multiple plots.
> >     One with just the outer_skin (opaque) and array (transparent) (I
> would
> >     prefer a sagittal view perhaps a view from the front is helpful too).
> >     Another one to five plots (multiple angles) of the outer skin
> >     (transparent) with the digitized points (scaled to indicate distance
> >     from the surface).
> >
> >     Paring down the amount of information shown in the Raw examples would
> >     be helpful.
> >
> >     I would also like to see a set order to the file (preferably based on
> >     a default flow for example: raw, -ave, -cov, trans, fwd, inv).
> >
> >     I would love to see the -eve file information included in the
> >     information with the raw information (in the same section). (even in
> >     cases where there is no -eve file (as find events can get this)).
> >
> >     I'd also like to see some of the names changed to make a better
> >     association with the actual filenames/filenaming conventions (this
> may
> >     prove to be controversial). For example Evoked -> Average (these are
> >     -ave.fif). Instead of MRI at the top right (maybe BEM).
> >
> >     But I would be happy to use this as is. It looks very good!
> >
> >     D
> >
> >     On Fri, Jul 11, 2014 at 12:27 PM, Alexandre Gramfort
> >     <alexandre.gramfort at telecom-paristech.fr
> >     <mailto:alexandre.gramfort at telecom-paristech.fr>> wrote:
> >     > hi,
> >     >
> >     > I am already really happy to see what Mainak has achieved but if
> you
> >     > think some relevant information is missing or not well highlighted,
> >     > it's the moment to ask so we can make it happen for the next
> release.
> >     >
> >     > Please take a minute to give some feedback and suggest
> improvements.
> >     >
> >     > Cheers,
> >     > Alex
> >     >
> >     >
> >     > On Fri, Jul 11, 2014 at 5:56 PM, Mainak Jas <mainak at neuro.hut.fi
> >     <mailto:mainak at neuro.hut.fi>> wrote:
> >     >> Dear all,
> >     >>
> >     >> We're converging on the `mne report` command that I was working
> >     for the
> >     >> Google Summer of Code this year.
> >     >>
> >     >> The idea is to run the `mne report` command as below:
> >     >>
> >     >> $ mne report --path MNE-sample-data/ --subjects-dir
> >     >> MNE-sample-data/subjects --subject sample
> >     >>
> >     >> providing it the data directory whose report must be created. It
> will
> >     >> generate a report as a single html file which can be easily
> >     shared with
> >     >> collaborators via email or dropbox. A link to the report
> >     generated from
> >     >> the MNE sample dataset is provided below:
> >     >>
> >     >> https://dl.dropboxusercontent.com/u/3915954/report.html
> >     >>
> >     >> The motivation is that it can be used to generate a quick
> >     >> summary/statistics of the results and do a quality check with
> minimal
> >     >> scripting. Typically, this is something one might want to run one
> day
> >     >> after data collection.
> >     >>
> >     >> We also provide a python interface for more advanced users who
> >     want to
> >     >> embed their own custom plots in the report.
> >     >>
> >     >> Any feedback towards improving this is most appreciated. Thanks!
> >     >>
> >     >> Best regards,
> >     >> Mainak
> >     >> _______________________________________________
> >     >> Mne_analysis mailing list
> >     >> Mne_analysis at nmr.mgh.harvard.edu
> >     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> >     >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >     >>
> >     >>
> >     >> The information in this e-mail is intended only for the person to
> >     whom it is
> >     >> addressed. If you believe this e-mail was sent to you in error
> >     and the e-mail
> >     >> contains patient information, please contact the Partners
> >     Compliance HelpLine at
> >     >> http://www.partners.org/complianceline . If the e-mail was sent
> >     to you in error
> >     >> but does not contain patient information, please contact the
> >     sender and properly
> >     >> dispose of the e-mail.
> >     >>
> >     > _______________________________________________
> >     > Mne_analysis mailing list
> >     > Mne_analysis at nmr.mgh.harvard.edu
> >     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> >     ------------------------------
> >
> >     Message: 5
> >     Date: Fri, 11 Jul 2014 20:34:44 +0200
> >     From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr
> >     <mailto:alexandre.gramfort at telecom-paristech.fr>>
> >     Subject: Re: [Mne_analysis] mne report command
> >     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.edu>>
> >     Message-ID:
> >
> >     <CADeotZo1itdrbyB+Ne9T7QdpnEq--8z3DE3Q+B6bc9Yk64raqg at mail.gmail.com
> >     <mailto:
> CADeotZo1itdrbyB%2BNe9T7QdpnEq--8z3DE3Q%2BB6bc9Yk64raqg at mail.gmail.com>>
> >     Content-Type: text/plain; charset=UTF-8
> >
> >     hi,
> >
> >     > By default don't include events with value of 0 (maybe include it
> as
> >     > an option). In most cases these are not true events.
> >
> >     the events are actually 1 not 0. This remark suggests me that we
> >     should not use standard y ticks/scaling for plot_events
> >
> >     > The covariance matrix scaling for gradiometers in the sample file
> >     seems flat.
> >
> >     I this it's correct. It's empty room with SSP applied.
> >
> >     > At least an option to force a scaling factor for each file type
> >     > (because it can be confusing for example that the left and right
> >     > visual evoked examples have different scalings for the
> gradiometers).
> >     >
> >     > It would be most helpful to split the Trans plot into multiple
> plots.
> >     > One with just the outer_skin (opaque) and array (transparent) (I
> would
> >     > prefer a sagittal view perhaps a view from the front is helpful
> too).
> >     > Another one to five plots (multiple angles) of the outer skin
> >     > (transparent) with the digitized points (scaled to indicate
> distance
> >     > from the surface).
> >
> >     we can indeed do better. Maybe you can take a look at the plot_trans
> >     function and improve it a bit?
> >
> >     > Paring down the amount of information shown in the Raw examples
> would
> >     > be helpful.
> >
> >     +1
> >
> >     > I would also like to see a set order to the file (preferably based
> on
> >     > a default flow for example: raw, -ave, -cov, trans, fwd, inv).
> >
> >     good point. +1
> >
> >     > I would love to see the -eve file information included in the
> >     > information with the raw information (in the same section). (even
> in
> >     > cases where there is no -eve file (as find events can get this)).
> >
> >     I like this too.
> >
> >     > I'd also like to see some of the names changed to make a better
> >     > association with the actual filenames/filenaming conventions (this
> may
> >     > prove to be controversial). For example Evoked -> Average (these
> are
> >     > -ave.fif). Instead of MRI at the top right (maybe BEM).
> >
> >     I suggested Evoked and MRI :) reason is that MRI can be displayed
> >     without BEM and Evoked can contain other things than average (std dev
> >     for example).
> >
> >     > But I would be happy to use this as is. It looks very good!
> >
> >     +1
> >
> >     again really nice job Mainak.
> >
> >     thanks heaps Dan for the valuable feedback.
> >
> >     Alex
> >
> >
> >     ------------------------------
> >
> >     _______________________________________________
> >     Mne_analysis mailing list
> >     Mne_analysis at nmr.mgh.harvard.edu
> >     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> >     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >     End of Mne_analysis Digest, Vol 78, Issue 20
> >     ********************************************
> >
> >
> >
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
>
>
> --
> Martin Luessi, Ph.D.
>
> Research Fellow
>
> Department of Radiology
> Athinoula A. Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Harvard Medical School
> 149 13th Street
> Charlestown, MA 02129
>
> Fax: +1 617 726-7422
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 19 Aug 2014 00:29:38 +0300
> From: Mainak Jas <mainakjas at gmail.com>
> Subject: Re: [Mne_analysis] Mne_analysis Digest, Vol 78, Issue 20
> To: Discussion and support forum for the users of MNE Software
>         <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
>         <CANzrpG1hGSSNChD3RCYTqW2mvoxvizvrBmh=
> 2Hm2m9uQPcorgw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Kambiz,
>
> You can get the mne report command in the latest mne-python release:
> https://pypi.python.org/pypi/mne/0.8.1.
>
> Mainak
>
> On Mon, Aug 18, 2014 at 11:59 PM, Martin Luessi <
> mluessi at nmr.mgh.harvard.edu
> > wrote:
>
> > Hi Kambiz,
> >
> > The report generator is part of MNE-Python, not the MNE command-line
> tools.
> >
> > Best,
> >
> > Martin
> >
> > On 08/18/14 16:52, Kambiz Tavabi wrote:
> > > hi all,
> > > I am using MNE-2.7.4-3439; I don't see the mne_report program in this
> > > build, nor in the 3443 build.
> > > Is there some other place the program is available? and if so can I get
> > > my hands on it? Thanks. Kam
> > >
> > > ------------------------------------------------------------
> > > Kambiz Tavabi PhD
> > > Institute for Learning & Brain Sciences
> > > 1715 Columbia Road N
> > > Portage Bay Building
> > > Box 357988
> > > University of Washington
> > > Seattle, WA 98195-7988
> > > Tel: 206-685-6173
> > > ------------------------------------------------------------
> > >
> > >
> > > On Fri, Jul 11, 2014 at 11:35 AM,
> > > <mne_analysis-request at nmr.mgh.harvard.edu
> > > <mailto:mne_analysis-request at nmr.mgh.harvard.edu>> wrote:
> > >
> > >     Send Mne_analysis mailing list submissions to
> > >             mne_analysis at nmr.mgh.harvard.edu
> > >     <mailto:mne_analysis at nmr.mgh.harvard.edu>
> > >
> > >     To subscribe or unsubscribe via the World Wide Web, visit
> > >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > >     or, via email, send a message with subject or body 'help' to
> > >             mne_analysis-request at nmr.mgh.harvard.edu
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> > >
> > >     You can reach the person managing the list at
> > >             mne_analysis-owner at nmr.mgh.harvard.edu
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> > >
> > >     When replying, please edit your Subject line so it is more specific
> > >     than "Re: Contents of Mne_analysis digest..."
> > >
> > >
> > >     Today's Topics:
> > >
> > >        1. mne report command (Mainak Jas)
> > >        2. Re: mne report command (Alexandre Gramfort)
> > >        3. Re: mne report command (Denis-Alexander Engemann)
> > >        4. Re: mne report command (dgw)
> > >        5. Re: mne report command (Alexandre Gramfort)
> > >
> > >
> > >
> >  ----------------------------------------------------------------------
> > >
> > >     Message: 1
> > >     Date: Fri, 11 Jul 2014 18:56:31 +0300 (EEST)
> > >     From: "Mainak Jas" <mainak at neuro.hut.fi <mailto:
> mainak at neuro.hut.fi
> > >>
> > >     Subject: [Mne_analysis] mne report command
> > >     To: mne_analysis at nmr.mgh.harvard.edu
> > >     <mailto:mne_analysis at nmr.mgh.harvard.edu>
> > >     Message-ID: <43974.82.130.26.44.1405094191.squirrel at neuro.hut.fi
> > >     <mailto:43974.82.130.26.44.1405094191.squirrel at neuro.hut.fi>>
> > >     Content-Type: text/plain;charset=iso-8859-1
> > >
> > >     Dear all,
> > >
> > >     We're converging on the `mne report` command that I was working for
> > the
> > >     Google Summer of Code this year.
> > >
> > >     The idea is to run the `mne report` command as below:
> > >
> > >     $ mne report --path MNE-sample-data/ --subjects-dir
> > >     MNE-sample-data/subjects --subject sample
> > >
> > >     providing it the data directory whose report must be created. It
> will
> > >     generate a report as a single html file which can be easily shared
> > with
> > >     collaborators via email or dropbox. A link to the report generated
> > from
> > >     the MNE sample dataset is provided below:
> > >
> > >     https://dl.dropboxusercontent.com/u/3915954/report.html
> > >
> > >     The motivation is that it can be used to generate a quick
> > >     summary/statistics of the results and do a quality check with
> minimal
> > >     scripting. Typically, this is something one might want to run one
> day
> > >     after data collection.
> > >
> > >     We also provide a python interface for more advanced users who want
> > to
> > >     embed their own custom plots in the report.
> > >
> > >     Any feedback towards improving this is most appreciated. Thanks!
> > >
> > >     Best regards,
> > >     Mainak
> > >
> > >
> > >     ------------------------------
> > >
> > >     Message: 2
> > >     Date: Fri, 11 Jul 2014 18:27:31 +0200
> > >     From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr
> > >     <mailto:alexandre.gramfort at telecom-paristech.fr>>
> > >     Subject: Re: [Mne_analysis] mne report command
> > >     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.edu>>
> > >     Message-ID:
> > >
> > >     <
> CADeotZqJvH5g1jqoUUwWKxa4FiP5M4MMOzVcTkfy9cvoFMd8Fw at mail.gmail.com
> > >     <mailto:
> > CADeotZqJvH5g1jqoUUwWKxa4FiP5M4MMOzVcTkfy9cvoFMd8Fw at mail.gmail.com>>
> > >     Content-Type: text/plain; charset=UTF-8
> > >
> > >     hi,
> > >
> > >     I am already really happy to see what Mainak has achieved but if
> you
> > >     think some relevant information is missing or not well highlighted,
> > >     it's the moment to ask so we can make it happen for the next
> release.
> > >
> > >     Please take a minute to give some feedback and suggest
> improvements.
> > >
> > >     Cheers,
> > >     Alex
> > >
> > >
> > >     On Fri, Jul 11, 2014 at 5:56 PM, Mainak Jas <mainak at neuro.hut.fi
> > >     <mailto:mainak at neuro.hut.fi>> wrote:
> > >     > Dear all,
> > >     >
> > >     > We're converging on the `mne report` command that I was working
> > >     for the
> > >     > Google Summer of Code this year.
> > >     >
> > >     > The idea is to run the `mne report` command as below:
> > >     >
> > >     > $ mne report --path MNE-sample-data/ --subjects-dir
> > >     > MNE-sample-data/subjects --subject sample
> > >     >
> > >     > providing it the data directory whose report must be created. It
> > will
> > >     > generate a report as a single html file which can be easily
> shared
> > >     with
> > >     > collaborators via email or dropbox. A link to the report
> generated
> > >     from
> > >     > the MNE sample dataset is provided below:
> > >     >
> > >     > https://dl.dropboxusercontent.com/u/3915954/report.html
> > >     >
> > >     > The motivation is that it can be used to generate a quick
> > >     > summary/statistics of the results and do a quality check with
> > minimal
> > >     > scripting. Typically, this is something one might want to run one
> > day
> > >     > after data collection.
> > >     >
> > >     > We also provide a python interface for more advanced users who
> > want to
> > >     > embed their own custom plots in the report.
> > >     >
> > >     > Any feedback towards improving this is most appreciated. Thanks!
> > >     >
> > >     > Best regards,
> > >     > Mainak
> > >     > _______________________________________________
> > >     > Mne_analysis mailing list
> > >     > Mne_analysis at nmr.mgh.harvard.edu
> > >     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> > >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > >     >
> > >     >
> > >     > The information in this e-mail is intended only for the person to
> > >     whom it is
> > >     > addressed. If you believe this e-mail was sent to you in error
> and
> > >     the e-mail
> > >     > contains patient information, please contact the Partners
> > >     Compliance HelpLine at
> > >     > http://www.partners.org/complianceline . If the e-mail was sent
> to
> > >     you in error
> > >     > but does not contain patient information, please contact the
> > >     sender and properly
> > >     > dispose of the e-mail.
> > >     >
> > >
> > >
> > >     ------------------------------
> > >
> > >     Message: 3
> > >     Date: Fri, 11 Jul 2014 18:44:28 +0200
> > >     From: Denis-Alexander Engemann <denis.engemann at gmail.com
> > >     <mailto:denis.engemann at gmail.com>>
> > >     Subject: Re: [Mne_analysis] mne report command
> > >     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.edu>>
> > >     Message-ID:
> > >
> > >     <
> CA+MN3Os+TROLw22hTMcK5G3VA+3KjQw6UCsPxBNZ99ztTbaivA at mail.gmail.com
> > >     <mailto:
> > CA%2BMN3Os%2BTROLw22hTMcK5G3VA%2B3KjQw6UCsPxBNZ99ztTbaivA at mail.gmail.com
> >>
> > >     Content-Type: text/plain; charset="utf-8"
> > >
> > >     Hi all,
> > >
> > >     here is an example that shows how to create a custom report:
> > >
> > >     https://gist.github.com/dengemann/dedbf84d07d79975d5a0
> > >
> > >     Best,
> > >     Denis
> > >
> > >
> > >     On Fri, Jul 11, 2014 at 6:27 PM, Alexandre Gramfort <
> > >     alexandre.gramfort at telecom-paristech.fr
> > >     <mailto:alexandre.gramfort at telecom-paristech.fr>> wrote:
> > >
> > >     > hi,
> > >     >
> > >     > I am already really happy to see what Mainak has achieved but if
> > you
> > >     > think some relevant information is missing or not well
> highlighted,
> > >     > it's the moment to ask so we can make it happen for the next
> > release.
> > >     >
> > >     > Please take a minute to give some feedback and suggest
> > improvements.
> > >     >
> > >     > Cheers,
> > >     > Alex
> > >     >
> > >     >
> > >     > On Fri, Jul 11, 2014 at 5:56 PM, Mainak Jas <mainak at neuro.hut.fi
> > >     <mailto:mainak at neuro.hut.fi>> wrote:
> > >     > > Dear all,
> > >     > >
> > >     > > We're converging on the `mne report` command that I was working
> > >     for the
> > >     > > Google Summer of Code this year.
> > >     > >
> > >     > > The idea is to run the `mne report` command as below:
> > >     > >
> > >     > > $ mne report --path MNE-sample-data/ --subjects-dir
> > >     > > MNE-sample-data/subjects --subject sample
> > >     > >
> > >     > > providing it the data directory whose report must be created.
> It
> > >     will
> > >     > > generate a report as a single html file which can be easily
> > >     shared with
> > >     > > collaborators via email or dropbox. A link to the report
> > >     generated from
> > >     > > the MNE sample dataset is provided below:
> > >     > >
> > >     > > https://dl.dropboxusercontent.com/u/3915954/report.html
> > >     > >
> > >     > > The motivation is that it can be used to generate a quick
> > >     > > summary/statistics of the results and do a quality check with
> > >     minimal
> > >     > > scripting. Typically, this is something one might want to run
> > >     one day
> > >     > > after data collection.
> > >     > >
> > >     > > We also provide a python interface for more advanced users who
> > >     want to
> > >     > > embed their own custom plots in the report.
> > >     > >
> > >     > > Any feedback towards improving this is most appreciated.
> Thanks!
> > >     > >
> > >     > > Best regards,
> > >     > > Mainak
> > >     > > _______________________________________________
> > >     > > Mne_analysis mailing list
> > >     > > Mne_analysis at nmr.mgh.harvard.edu
> > >     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> > >     > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > >     > >
> > >     > >
> > >     > > The information in this e-mail is intended only for the person
> > >     to whom
> > >     > it is
> > >     > > addressed. If you believe this e-mail was sent to you in error
> > >     and the
> > >     > e-mail
> > >     > > contains patient information, please contact the Partners
> > Compliance
> > >     > HelpLine at
> > >     > > http://www.partners.org/complianceline . If the e-mail was
> sent
> > >     to you
> > >     > in error
> > >     > > but does not contain patient information, please contact the
> > >     sender and
> > >     > properly
> > >     > > dispose of the e-mail.
> > >     > >
> > >     > _______________________________________________
> > >     > Mne_analysis mailing list
> > >     > Mne_analysis at nmr.mgh.harvard.edu
> > >     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> > >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > >     >
> > >     -------------- next part --------------
> > >     An HTML attachment was scrubbed...
> > >     URL:
> > >
> >
> http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140711/a59d133a/attachment-0001.html
> > >
> > >     ------------------------------
> > >
> > >     Message: 4
> > >     Date: Fri, 11 Jul 2014 13:23:04 -0400
> > >     From: dgw <dgwakeman at gmail.com <mailto:dgwakeman at gmail.com>>
> > >     Subject: Re: [Mne_analysis] mne report command
> > >     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.edu>>
> > >     Message-ID:
> > >
> > >     <
> CADM2BTj5+c-ber6YWJ52NJvTzWS_iyt_sA-CQ94D_eMnPYMK4w at mail.gmail.com
> > >     <mailto:
> > CADM2BTj5%2Bc-ber6YWJ52NJvTzWS_iyt_sA-CQ94D_eMnPYMK4w at mail.gmail.com>>
> > >     Content-Type: text/plain; charset=UTF-8
> > >
> > >     Hi Mainak,
> > >
> > >     This looks great!
> > >
> > >     My suggestions:
> > >
> > >     Remove the full path from the names of each file (just put the path
> > at
> > >     the top of the report).
> > >     No space between the colon and file type:
> > >     Events : MNE-sample-data/MEG/sample/ernoise_raw-eve.fif -> Events:
> > >     ernoise_raw-eve.fif
> > >
> > >     By default don't include events with value of 0 (maybe include it
> as
> > >     an option). In most cases these are not true events.
> > >
> > >     The covariance matrix scaling for gradiometers in the sample file
> > >     seems flat.
> > >
> > >     At least an option to force a scaling factor for each file type
> > >     (because it can be confusing for example that the left and right
> > >     visual evoked examples have different scalings for the
> gradiometers).
> > >
> > >     It would be most helpful to split the Trans plot into multiple
> plots.
> > >     One with just the outer_skin (opaque) and array (transparent) (I
> > would
> > >     prefer a sagittal view perhaps a view from the front is helpful
> too).
> > >     Another one to five plots (multiple angles) of the outer skin
> > >     (transparent) with the digitized points (scaled to indicate
> distance
> > >     from the surface).
> > >
> > >     Paring down the amount of information shown in the Raw examples
> would
> > >     be helpful.
> > >
> > >     I would also like to see a set order to the file (preferably based
> on
> > >     a default flow for example: raw, -ave, -cov, trans, fwd, inv).
> > >
> > >     I would love to see the -eve file information included in the
> > >     information with the raw information (in the same section). (even
> in
> > >     cases where there is no -eve file (as find events can get this)).
> > >
> > >     I'd also like to see some of the names changed to make a better
> > >     association with the actual filenames/filenaming conventions (this
> > may
> > >     prove to be controversial). For example Evoked -> Average (these
> are
> > >     -ave.fif). Instead of MRI at the top right (maybe BEM).
> > >
> > >     But I would be happy to use this as is. It looks very good!
> > >
> > >     D
> > >
> > >     On Fri, Jul 11, 2014 at 12:27 PM, Alexandre Gramfort
> > >     <alexandre.gramfort at telecom-paristech.fr
> > >     <mailto:alexandre.gramfort at telecom-paristech.fr>> wrote:
> > >     > hi,
> > >     >
> > >     > I am already really happy to see what Mainak has achieved but if
> > you
> > >     > think some relevant information is missing or not well
> highlighted,
> > >     > it's the moment to ask so we can make it happen for the next
> > release.
> > >     >
> > >     > Please take a minute to give some feedback and suggest
> > improvements.
> > >     >
> > >     > Cheers,
> > >     > Alex
> > >     >
> > >     >
> > >     > On Fri, Jul 11, 2014 at 5:56 PM, Mainak Jas <mainak at neuro.hut.fi
> > >     <mailto:mainak at neuro.hut.fi>> wrote:
> > >     >> Dear all,
> > >     >>
> > >     >> We're converging on the `mne report` command that I was working
> > >     for the
> > >     >> Google Summer of Code this year.
> > >     >>
> > >     >> The idea is to run the `mne report` command as below:
> > >     >>
> > >     >> $ mne report --path MNE-sample-data/ --subjects-dir
> > >     >> MNE-sample-data/subjects --subject sample
> > >     >>
> > >     >> providing it the data directory whose report must be created. It
> > will
> > >     >> generate a report as a single html file which can be easily
> > >     shared with
> > >     >> collaborators via email or dropbox. A link to the report
> > >     generated from
> > >     >> the MNE sample dataset is provided below:
> > >     >>
> > >     >> https://dl.dropboxusercontent.com/u/3915954/report.html
> > >     >>
> > >     >> The motivation is that it can be used to generate a quick
> > >     >> summary/statistics of the results and do a quality check with
> > minimal
> > >     >> scripting. Typically, this is something one might want to run
> one
> > day
> > >     >> after data collection.
> > >     >>
> > >     >> We also provide a python interface for more advanced users who
> > >     want to
> > >     >> embed their own custom plots in the report.
> > >     >>
> > >     >> Any feedback towards improving this is most appreciated. Thanks!
> > >     >>
> > >     >> Best regards,
> > >     >> Mainak
> > >     >> _______________________________________________
> > >     >> Mne_analysis mailing list
> > >     >> Mne_analysis at nmr.mgh.harvard.edu
> > >     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> > >     >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > >     >>
> > >     >>
> > >     >> The information in this e-mail is intended only for the person
> to
> > >     whom it is
> > >     >> addressed. If you believe this e-mail was sent to you in error
> > >     and the e-mail
> > >     >> contains patient information, please contact the Partners
> > >     Compliance HelpLine at
> > >     >> http://www.partners.org/complianceline . If the e-mail was sent
> > >     to you in error
> > >     >> but does not contain patient information, please contact the
> > >     sender and properly
> > >     >> dispose of the e-mail.
> > >     >>
> > >     > _______________________________________________
> > >     > Mne_analysis mailing list
> > >     > Mne_analysis at nmr.mgh.harvard.edu
> > >     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> > >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > >
> > >
> > >     ------------------------------
> > >
> > >     Message: 5
> > >     Date: Fri, 11 Jul 2014 20:34:44 +0200
> > >     From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr
> > >     <mailto:alexandre.gramfort at telecom-paristech.fr>>
> > >     Subject: Re: [Mne_analysis] mne report command
> > >     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.edu>>
> > >     Message-ID:
> > >
> > >     <
> CADeotZo1itdrbyB+Ne9T7QdpnEq--8z3DE3Q+B6bc9Yk64raqg at mail.gmail.com
> > >     <mailto:
> > CADeotZo1itdrbyB%2BNe9T7QdpnEq--8z3DE3Q%2BB6bc9Yk64raqg at mail.gmail.com>>
> > >     Content-Type: text/plain; charset=UTF-8
> > >
> > >     hi,
> > >
> > >     > By default don't include events with value of 0 (maybe include it
> > as
> > >     > an option). In most cases these are not true events.
> > >
> > >     the events are actually 1 not 0. This remark suggests me that we
> > >     should not use standard y ticks/scaling for plot_events
> > >
> > >     > The covariance matrix scaling for gradiometers in the sample file
> > >     seems flat.
> > >
> > >     I this it's correct. It's empty room with SSP applied.
> > >
> > >     > At least an option to force a scaling factor for each file type
> > >     > (because it can be confusing for example that the left and right
> > >     > visual evoked examples have different scalings for the
> > gradiometers).
> > >     >
> > >     > It would be most helpful to split the Trans plot into multiple
> > plots.
> > >     > One with just the outer_skin (opaque) and array (transparent) (I
> > would
> > >     > prefer a sagittal view perhaps a view from the front is helpful
> > too).
> > >     > Another one to five plots (multiple angles) of the outer skin
> > >     > (transparent) with the digitized points (scaled to indicate
> > distance
> > >     > from the surface).
> > >
> > >     we can indeed do better. Maybe you can take a look at the
> plot_trans
> > >     function and improve it a bit?
> > >
> > >     > Paring down the amount of information shown in the Raw examples
> > would
> > >     > be helpful.
> > >
> > >     +1
> > >
> > >     > I would also like to see a set order to the file (preferably
> based
> > on
> > >     > a default flow for example: raw, -ave, -cov, trans, fwd, inv).
> > >
> > >     good point. +1
> > >
> > >     > I would love to see the -eve file information included in the
> > >     > information with the raw information (in the same section). (even
> > in
> > >     > cases where there is no -eve file (as find events can get this)).
> > >
> > >     I like this too.
> > >
> > >     > I'd also like to see some of the names changed to make a better
> > >     > association with the actual filenames/filenaming conventions
> (this
> > may
> > >     > prove to be controversial). For example Evoked -> Average (these
> > are
> > >     > -ave.fif). Instead of MRI at the top right (maybe BEM).
> > >
> > >     I suggested Evoked and MRI :) reason is that MRI can be displayed
> > >     without BEM and Evoked can contain other things than average (std
> dev
> > >     for example).
> > >
> > >     > But I would be happy to use this as is. It looks very good!
> > >
> > >     +1
> > >
> > >     again really nice job Mainak.
> > >
> > >     thanks heaps Dan for the valuable feedback.
> > >
> > >     Alex
> > >
> > >
> > >     ------------------------------
> > >
> > >     _______________________________________________
> > >     Mne_analysis mailing list
> > >     Mne_analysis at nmr.mgh.harvard.edu
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> > >     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > >
> > >     End of Mne_analysis Digest, Vol 78, Issue 20
> > >     ********************************************
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Mne_analysis mailing list
> > > Mne_analysis at nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > >
> >
> >
> > --
> > Martin Luessi, Ph.D.
> >
> > Research Fellow
> >
> > Department of Radiology
> > Athinoula A. Martinos Center for Biomedical Imaging
> > Massachusetts General Hospital
> > Harvard Medical School
> > 149 13th Street
> > Charlestown, MA 02129
> >
> > Fax: +1 617 726-7422
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