[Mne_analysis] Mne_analysis Digest, Vol 78, Issue 20
Mainak Jas
mainakjas at gmail.com
Mon Aug 18 17:29:38 EDT 2014
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
> > <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
> _______________________________________________
> Mne_analysis mailing list
> 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/20140819/d89fb6f5/attachment.html
More information about the Mne_analysis
mailing list