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