[Mne_analysis] Baseline calculation

Stephen Politzer-Ahles politzerahless at gmail.com
Fri Mar 30 16:28:57 EDT 2012
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Reid,

I see. I imagine it would be possible to do baseline-correction in MATLAB
since you have a list of the latencies of each trigger (I personally don't
have experience working with the MNE MATLAB toolbox, but once you've gotten
the data into MATLAB then I imagine doing the baseline-correction should be
straightforward if you're familiar with MATLAB itself: just iterating
through each trial, selecting the proper latency from that trial from your
list, and calculating and applying a baseline-correction based on the
specific latency for that trial, then saving the data and exporting back
out to .fif). I'm not aware of a way to do this with MNE functions,
although someone else on the list might be.

Best,
Steve

On Fri, Mar 30, 2012 at 3:20 PM, Vancelette, Reid Vincent <
RVANCELETTE at partners.org> wrote:

>  Hi Steven and everyone else,****
>
> ** **
>
> We used auditory presentation for our study. This means that the latencies
> vary depending on the word and the sentence. We unfortunately didn’t
> normalize all of the lengths of all the segments so that the matched. Is
> there any way to go around this problem? I know the lengths of each of the
> segments in all of the sentences: this is how we initially created the
> triggers for our experiment. ****
>
> ** **
>
> -Reid****
>
> ** **
>
> *From:* Stephen Politzer-Ahles [mailto:politzerahless at gmail.com]
> *Sent:* Friday, March 30, 2012 5:19 AM
> *To:* Vancelette, Reid Vincent
> *Cc:* mne_analysis at nmr.mgh.harvard.edu
> *Subject:* Re: [Mne_analysis] Baseline calculation****
>
> ** **
>
> Hi Vancelette,
>
> Is the time between the beginning of a sentence and a given trigger always
> the same across items? (That should be the case if the number of words is
> always the same and you used serial visual presentation; if the position of
> a given trigger varies across items and/or you used auditory presentation,
> though, then the latencies probably vary.) If this latency is always the
> same then you can just add that latency to what the baseline interval would
> be for each trigger. For instance, if the baseline for the first trigger
> were -100 to 0, and the second trigger always appeared 800 ms after the
> first, then the baseline for the second could be -900 to -800.
>
> Best,
> Steve****
>
> On Thu, Mar 29, 2012 at 10:42 AM, Vancelette, Reid Vincent <
> RVANCELETTE at partners.org> wrote:****
>
> Hi all,****
>
>  ****
>
> I am currently in the process of performing preprocessing on my MEG/EEG
> data and am trying to correctly calculate a baseline. I am working with
> whole sentences that have several triggers within each sentence to mark
> particular areas of interest (for example: the noun, the verb). The current
> way that we calculate the baseline is from 100 ms before each of the
> triggers. Is there any way that I can calculate the baseline from the first
> trigger of each of the sentences (which happens to correspond to the
> beginning of the sentence) and apply that to each of the triggers within
> that particular sentence instead of having to calculate it 100 ms before
> each of the triggers? I am asking this because as of right now we are
> basically forced to calculate the baseline while the subject is hearing the
> sentences, which can bias the data. ****
>
>  ****
>
> Thanks in advance,****
>
>  ****
>
> Reid****
>
>  ****
>
> Reid Vancelette****
>
> Research Assistant to****
>
> Dr. David Caplan M.D., Ph.D.****
>
>  ****
>
> Massachusetts General Hospital****
>
> Neuropsychology Lab****
>
> 175 Cambridge Street, Suite 340****
>
> Boston, MA 02114****
>
>  ****
>
> Phone: (617) 724-8846****
>
> Email: rvancelette at partners.org****
>
>  ****
>
>  ****
>
>
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>
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://www.linguistics.ku.edu/****
>



-- 
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://www.linguistics.ku.edu/
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