[Mne_analysis] Mne_analysis Digest, Vol 78, Issue 20
Martin Luessi
mluessi at nmr.mgh.harvard.edu
Mon Aug 18 16:59:38 EDT 2014
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
More information about the Mne_analysis
mailing list