[Mne_analysis] magflat and gradflat in mne_process_raw

[sheraz at nmr.mgh.harvard.edu]

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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>>
>>
>> --
>> 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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