about biosig folder

jan-mathijs schoffelen j.schoffelen at PSY.GLA.AC.UK
Thu Apr 23 09:48:07 CEST 2009


Dear Jim,

Yes, I suspect that you just can remove the biosig folder from your
path. As long as you don't use fieldtrip functionality which depends
on functions within the biosig-folder you are fine.


Yours,

JM

On Apr 22, 2009, at 5:12 PM, Jim Li wrote:

> Dear Jan-Mathijs,
>
> Following your recommendation, I downloaded the 041809 Fieldtrip
> and it
> reads our data just fine. I'll keep an eye on the outputs as I
> advance more
> into the data processing and report suspicious ones, if any.
>
> BTW, w/ this new version I get a bunch of annoying messages each
> time I
> open MATLAB. What I did is to add this new version of Fieldtrip in
> MATLAB by
> clicking "Set Path" and "Add with subfolders...". And the warning
> messages
> look like this (just one warning example out of a zillion):
>
> ----
> Warning: Function C:\Program
> Files\MATLAB\R2007b\external\fieldtrip-20090418
> \external\biosig\private\transpose.m
> has the same name as a MATLAB builtin. We suggest you rename the
> function
> to
> avoid a potential name conflict.
>> In path at 110
>   In addpath at 89
>   In startup at 1
>   In matlabrc at 251
> ---
>
> All the warning is related to the "fieldtrip-20090418\external
> \biosig\private\"
> directory. So, what's the use of this "biosig" folder? Can I just
> remove it from
> my "MATLAB search Path" w/o affecting Fieldtrip operations?
>
> Thanks,
>
> Jim
>
> On Tue, 21 Apr 2009 09:22:05 +0100, jan-mathijs schoffelen
> <j.schoffelen at PSY.GLA.AC.UK> wrote:
>
>> Dear Julian and other 4D-neuroimagers,
>>
>> Thanks for your feedback. There have been some changes in read_4d_hdr
>> bti2grad which might affect performance though, so I would greatly
>> appreciate if you could upgrade to the latest version and see if you
>> are still happy.
>> In a nutshell it boils down to the fact that read_4d_hdr tries to
>> extract the digital weights from the run config-file which were used
>> during acquisition. So far, these weights have not been included in
>> the forward modelling, which is necessary for dipole fitting / source
>> reconstruction. Although I don't expect that the inclusion of the
>> weights (which are a function of the distant reference sensors, and
>> hardly pick up any brain activity to begin with) is going to affect
>> the leadfields to a big extent, not including them is not completely
>> correct.
>> As far as I know (and thanks to Stephan Moratti for pointing it out
>> and Sarang Dalal for some code) there are two versions of the weight-
>> tables which roughly seem to coincide with the type of system:
>> version 1 (number of observations = 1.5: Madrid 148-magnetometer, and
>> most likely also the Konstanz system), and version 2 (number of
>> observations = 1: Glasgow 248-magnetometer). To make a long story
>> short, the version 1 weight table just seems to contain the weights,
>> and no specific list of channel labels facilitating the
>> interpretation of the weights. This is in contrast to the version 2
>> table, which contains the lists of labels explicitly. Therefore, we
>> would have to guess about the order of the channels and reference
>> channels occurring in the version 1 weight matrix. I'd rather not
>> guess, and prefer to base some hard-coded assumptions on some
>> (pragmatically 1 or 2 ;o) ) observations...
>> This means I would like to compare the list of weights as obtained
>> with read_4d_hdr to the list of weights which the 4D-software should
>> be able to print (I thought the command was something like
>> print_table, or print_config or so). More specifically, given a
>> particular recording in which for example 'supine' weights had been
>> applied, we should compare the 'supine' weight table, to the weights
>> extracted by fieldtrip. In that way we could gain some confidence
>> about the order of the channels.
>> Please note that at the moment no balancing is applied to data
>> containing a 'version 1' weight table, at least if you use a
>> fieldtrip version older than March 26, or more recent than April 2.
>>
>> Yours,
>>
>> Jan-Mathijs
>>
>> On Apr 21, 2009, at 8:07 AM, Julian Keil wrote:
>>
>>> Dear Jan,
>>>
>>> the read_4d_hdr also works quite nicely for the Konstanz 148-
>>> magnetometer site as far as I can tell.
>>> I currently use the 2009-03-22 version of fieldtrip.
>>>
>>> Greetings
>>>
>>> Julian
>>>
>>> Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen:
>>>
>>>> Dear Jim,
>>>>
>>>> I'd be happy to try and sort out problems with respect to my
>>>> intended improvement of read_4d_hdr, because I assume there were
>>>> some problems initially? It was kind of a bold commit into
>>>> fieldtrip, I admit that, because I wasn't sure what this would
>>>> lead to. My intention was partly to spark the involvement of 4D
>>>> MEG users at other sites so that we could jointly improve the
>>>> robustness of the code. So far all seems to work well for the
>>>> Glaswegian 248-magnetometer site, but I am pretty sure this is not
>>>> the case for all 4D-systems roaming the face of the earth... I
>>>> would greatly appreciate if you try the most recent fieldtrip
>>>> version on your data and provide me with feedback and possibly
>>>> suggestions for improvement of the code.
>>>>
>>>> Cheers,
>>>>
>>>> Jan-Mathijs
>>>>
>>>>
>>>> On Apr 20, 2009, at 10:13 PM, Jim Li wrote:
>>>>
>>>>> Dear Jan-Mathijs,
>>>>>
>>>>> Thanks a lot for your answer. I see why my "componentanalysis"
>>>>> didn't work
>>>>> w/o downloading EEGLAB now:
>>>>>
>>>>> As users of a 4D system, I'm avoiding your new updated version of
>>>>> read_4d_hdr by sticking to some old (Dec. 2008) version of
>>>>> Fieldtrip, simply
>>>>> because it's been working fine and I'm lazy. But apparently
>>>>> there's
>>>>> no "external/eeglab" subfolder in those old versions (yes, I have
>>>>> several Dec
>>>>> 08 versions). That's why I had to download EEGLAB to get it to
>>>>> work. I
>>>>> wonder since when did you add the subfolder to Fieldtrip?
>>>>>
>>>>> Anyway, I guess it's time to embrace the new Fieldtrip versions
>>>>> and learn the
>>>>> new way to read 4D data.
>>>>>
>>>>> Thanks a  lot for your help, :)
>>>>>
>>>>> Jim
>>>>>
>>>>>
>>>>> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen
>>>>> <j.schoffelen at PSY.GLA.AC.UK> wrote:
>>>>>
>>>>>> Dear Jim,
>>>>>>
>>>>>> I don't know whether I understand your question correctly, but
>>>>>> Fieldtrip can do it 'without' a full download of EEGLAB, because
>>>>>> the
>>>>>> necessary ICA-routines are included in fieldtrip's download (and
>>>>>> are
>>>>>> located in the subfolder external/eeglab/... This means that your
>>>>>> mystery someone was right ;o)
>>>>>>
>>>>>> Cheers,
>>>>>> Jan-Mathijs
>>>>>>
>>>>>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote:
>>>>>>
>>>>>>> Dear all,
>>>>>>>
>>>>>>> I'm trying to remove cardiac interferences from my MEG signal
>>>>>>> (gradiometer)
>>>>>>> channels before doing wavelet analysis. This seems necessary
>>>>>>> because, when
>>>>>>> looking at each epoch, the wavelet power @ 10-40Hz are
>>>>>>> dominated by
>>>>>>> cardiac interference, and that's the bandwidth of interest. I
>>>>>>> see
>>>>>>> some Fieldtrip
>>>>>>> example script utilizing ICA of EEGLAB to remove cardiac
>>>>>>> interference.
>>>>>>> However, someone told me that it can be done in Fieldtrip w/o
>>>>>>> using
>>>>>>> EEGLAB.
>>>>>>> Is this true? If so, I'd appreciate it very much if anyone can
>>>>>>> send
>>>>>>> me the
>>>>>>> code, :)
>>>>>>>
>>>>>>> Thanks a lot,
>>>>>>>
>>>>>>> Jim
>>>>>>>
>>>>>>> ----------------------------------
>>>>>>> The aim of this list is to facilitate the discussion between
>>>>>>> users
>>>>>>> of the FieldTrip  toolbox, to share experiences and to
>>>>>>> discuss new
>>>>>>> ideas for MEG and EEG analysis. See also http://
>>>>>>> listserv.surfnet.nl/
>>>>>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/
>>>>>>> fieldtrip.
>>>>>>
>>>>>> ----------------------------------
>>>>>> The aim of this list is to facilitate the discussion between
>>>>>> users of the
>>>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>>>>> for MEG and
>>>>> EEG analysis. See also http://listserv.surfnet.nl/archives/
>>>>> fieldtrip.html and
>>>>> http://www.ru.nl/neuroimaging/fieldtrip.
>>>>>
>>>>> ----------------------------------
>>>>> The aim of this list is to facilitate the discussion between
>>>>> users of the FieldTrip  toolbox, to share experiences and to
>>>>> discuss new ideas for MEG and EEG analysis. See also http://
>>>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
>>>>> neuroimaging/fieldtrip.
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>>> of the FieldTrip  toolbox, to share experiences and to discuss new
>>>> ideas for MEG and EEG analysis. See also http://
>>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
>>>> neuroimaging/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>>> of the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and
> EEG analysis. See also http://listserv.surfnet.nl/archives/
> fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.



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