[Mne_analysis] Baseline calculation
dgw
dgwakeman at gmail.com
Fri Mar 30 16:41:34 EDT 2012
I agree, something along those lines is probably easiest.
For future experiments, there are better options for designing your
triggers, which will make these sorts of calculations simpler.
D
Stephen Politzer-Ahles wrote:
> 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 <mailto: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
> <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
> <mailto: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 <mailto: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 <tel:%28617%29%20724-8846>____
>
> Email: rvancelette at partners.org <mailto: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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