[Mne_analysis] magflat and gradflat in mne_process_raw

[Matti Hamalainen]

Actually, MNE-Python may have projection calculations, too.

- 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
>>>>> 
>>>>> 
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>>>> 
>>>> ---------
>>>> 
>>>> Matti Hamalainen, Ph.D.
>>>> Athinoula A. Martinos Center for Biomedical Imaging
>>>> Massachusetts General Hospital
>>>> 
>>>> msh at nmr.mgh.harvard.edu
>>>> mhamalainen at partners.org
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
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>>>> Mne_analysis at nmr.mgh.harvard.edu
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>>> 
>>> 
>>> --
>>> 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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