[Mne_analysis] mne report command

dgw dgwakeman at gmail.com
Fri Jul 11 13:23:04 EDT 2014
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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:

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!


On Fri, Jul 11, 2014 at 12:27 PM, Alexandre Gramfort
<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> 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
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