[Mne_analysis] magflat and gradflat in mne_process_raw

[Alexandre Gramfort]

hi,

indeed it's doable with mne-python although the command line tool :

https://github.com/mne-tools/mne-python/blob/master/bin/mne_compute_proj_ecg.py

to compute automatically ECG / EOG projections does not support yes flat params.

In order not to forget I've opened in issue:

https://github.com/mne-tools/mne-python/issues/92

In the future for bug reports and feature requests do not hesitate to
open an issue on github.

Best,
Alex


On Sat, Sep 8, 2012 at 11:30 PM, Martin Luessi
<mluessi at nmr.mgh.harvard.edu> wrote:
> On 09/08/12 13:38, Matti Hamalainen wrote:
>> Actually, MNE-Python may have projection calculations, too.
>
> Yes, mne-python has scrips to compute SSP projectors for ECG and EOG.
> Assuming you have mne-python set up*, run "mne_compute_proj_eog.py
> --help" from the command line to see the available options. The script
> will detect EOG events and then compute projectors. The script doesn't
> have the option to discard flat sections, but if the EOG channels are
> flat, there won't be any events.
>
>
> Martin
>
> *see
> http://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide/NMRCenterPython/UsersGuide
> for instructions
>
>
>> - Matti
>>
>> On Sep 8, 2012, at 13:28, sheraz at nmr.mgh.harvard.edu wrote:
>>
>>> Hi Candida,
>>> couple of years back, I wrote a function in Matlab that compute
>>> projections from raw fif file on supplied event file and store them in mne
>>> format. In Matlab we can custom the kind of data rejection you want.
>>>
>>> Feel free to pass-by for it.
>>>
>>> Sheraz
>>>
>>>> Great idea! I forgot that mne_cov2proj exists.
>>>>
>>>> - Matti
>>>>
>>>> On Sep 8, 2012, at 12:12, "Hari Bharadwaj" <hari at nmr.mgh.harvard.edu>
>>>> wrote:
>>>>
>>>>> ,
>>>>>   Perhaps you could make SSPs in 2 steps:
>>>>> (1) Make a cov file for your blinks using a cov descriptor where you can
>>>>> specify flat channel limits
>>>>> (2) Use mne_cov2proj
>>>>>
>>>>> Regards,
>>>>> Hari
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Sat, September 8, 2012 8:07 am, Matti Hamalainen wrote:
>>>>>>
>>>>>> There is no way to specify the "flat" limits on the command line of
>>>>>> mne_process_raw, unfortunately.
>>>>>>
>>>>>> However, in the Averaging preferences dialog (Adjust menu) of
>>>>>> mne_browse_raw there are "no signal" limits  (flat parameters) which
>>>>>> affect the interactive computation of the projection operators.
>>>>>>
>>>>>> - Matti
>>>>>>
>>>>>> On Sep 7, 2012, at 3:46 PM, Candida Jane Maria Ustine wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I am working on removing the blink artifact using the PCA in mne. We
>>>>>>> have a couple of subjects whose channels go flat for a few
>>>>>>> seconds(EEG,
>>>>>>> MEG, EOG and ECG) including the stimuli. I was wondering if there is a
>>>>>>> way to skip that part of the raw.fif file while using the
>>>>>>> mne_process_raw command to create an EOG projector.
>>>>>>>
>>>>>>> I was wondering if this skip can be done when we create a projector
>>>>>>> just
>>>>>>> like how we can introduce a descriptor file when we are creating
>>>>>>> averages using mne_process_raw. I wanted to know of
>>>>>>> gradflat/magflat/eegflat parameters can be included in the
>>>>>>> mne_process_raw command. (I don't think this option is there in the
>>>>>>> mne_browse_raw gui structure.)
>>>>>>>
>>>>>>> Do let me know if there is another way of omitting the blank data in
>>>>>>> the
>>>>>>> fif file when creating a projector.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Candida
>>>>>>>
>>>>>>> --
>>>>>>> Candida Jane Maria Ustine M.Eng.
>>>>>>> NeuroCognition Lab
>>>>>>> Athinoula A. Martinos Center of Biomedical Imaging
>>>>>>> Department of Psychiatry - Neurosciences
>>>>>>> Massachusetts General Hospital
>>>>>>> candida at nmr.mgh.harvard.edu
>>>>>>>
>>>>>>>
>>>>>>> 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
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>>>>>>> e-mail.
>>>>>>>
>>>>>>
>>>>>> ---------
>>>>>>
>>>>>> Matti Hamalainen, Ph.D.
>>>>>> Athinoula A. Martinos Center for Biomedical Imaging
>>>>>> Massachusetts General Hospital
>>>>>>
>>>>>> msh at nmr.mgh.harvard.edu
>>>>>> mhamalainen at partners.org
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Mne_analysis mailing list
>>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>
>>>>>
>>>>> --
>>>>> Hari Bharadwaj
>>>>> PhD Candidate, Biomedical Engineering,
>>>>> Boston University
>>>>> 677 Beacon St.,
>>>>> Boston, MA 02215
>>>>>
>>>>> Martinos Center for Biomedical Imaging,
>>>>> Massachusetts General Hospital
>>>>> 149 Thirteenth Street,
>>>>> Charlestown, MA 02129
>>>>>
>>>>> hari at nmr.mgh.harvard.edu
>>>>> Ph: 734-883-5954
>>>>>
>>>>>
>>>>>
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