[FieldTrip] Problems with Neuromag Data after SSS

Stephan Moratti smoratti at psi.ucm.es
Mon Jun 20 08:26:46 CEST 2011


Dear Vladimir,

Thanks for this hint. I will check this!

Best,

Stephan

El 19/06/2011, a las 21:08, Vladimir Litvak escribió:

> Dear Stephan,
>
> It might be that or that you transferred the files as ascii in FTP
> rather than binary. I've seen this error before and showed the file to
> Matti Hamalainen. He said the file was corrupted.
>
> Best,
>
> Vladimir
>
> On Sun, Jun 19, 2011 at 4:20 PM, Stephan Moratti  
> <smoratti at psi.ucm.es> wrote:
>> Hi Lauren,
>> Thanks for your reply. Yes I had it with 6 data sets where SSS was  
>> applied.
>> I had them copied from the HP workstation to our server and from  
>> there to my
>> Mac. Could it be a little and big endian thing provoked by moving  
>> the files
>> from different platforms?
>> Stephan
>> El 17/06/2011, a las 9:28, Laurence Hunt escribió:
>>
>> Hi Stephan,
>> Did you do anything else to the data besides applying SSS? I use  
>> SSS on all
>> my data and haven't encountered this problem before. Does it apply  
>> to all
>> your datasets or just one specific file?
>> Laurence
>> ===========================================
>> Laurence Hunt, DPhil Student
>>  Centre for Functional MRI of the Brain (FMRIB),
>> University of Oxford
>> lhunt at fmrib.ox.ac.uk
>> Phone: (+44)1865-(2)22738
>> ===========================================
>> On 17 Jun 2011, at 08:01, Stephan Moratti wrote:
>>
>> Hello everybody,
>> I had no problems reading Neuromag data, but when I want to read data
>> treated with SSS I get the following error:
>> ??? Error using ==> fiff_read_tag at 232
>> Cannot handle other than dense or sparse matrices yet
>> Error in ==> fiff_open at 80
>>     tag = fiff_read_tag(fid,dirpos);
>> Error in ==> fiff_read_meas_info at 82
>>     [ fid, tree ] = fiff_open(source);
>> Error in ==> ft_read_header at 1049
>>     orig = fiff_read_meas_info(filename);
>> Error in ==> mytrialfun_Neuromag_face at 3
>> hdr = ft_read_header(cfg.dataset);
>> Error in ==> ft_definetrial at 139
>>     trl   = feval(cfg.trialfun, cfg);
>> Any idea, what I could do?
>> Best,
>> Stephan
>>
>> El 17/06/2011, a las 0:37, Rodolphe Nenert escribió:
>>
>> Im still afraid that the power of this analysis will be very low.
>> Maybe you can try an ICA on your fMRI data and try to correlate each
>> component with your EOG timecourse.
>> Rodolphe N.
>>
>> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net <fieldtrip at greenant.net 
>> >
>> wrote:
>>>
>>> It's a bit of a unique experiment, we're trying to use an ECG  
>>> machine
>>> to acquire EOG, so it's only a single output channel.
>>> i guess what I need is a temporal ICA rather than a spatial one...
>>> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote:
>>>
>>> To summarize, the ICA will decompose your signal into as many  
>>> components
>>> as Electrodes.
>>> Therefore, trying to decompose only one source is useless.
>>> Did you use a full net of electrodes into your MRI machine or only  
>>> EOG
>>> electrodes?
>>> Hope this helps,
>>> Rodolphe N.
>>>
>>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net
>>> <fieldtrip at greenant.net> wrote:
>>>>
>>>> I am trying to use fieldtrip to filter EOG data obtained in an MRI.
>>>> I want to be able to spot the saccades in the samples and ideally  
>>>> measure
>>>> their onset at the
>>>> end of each trial.
>>>>
>>>> As you may guess, it's quite noisy and it's broad spectrum noise,  
>>>> despite
>>>> pre-filtering.
>>>>
>>>> Ideally, I would like to isolate the component that corresponds  
>>>> to the
>>>> MRI interference
>>>> and then filter this out.
>>>>
>>>> I have managed to import the data and can run ft_componentanalysis
>>>> but it fails with:
>>>>
>>>> runica() - data size (1,30720) too small
>>>>
>>>> My data is single channel, 40 epochs, each of 6 seconds (time  
>>>> locked to
>>>> stim onset but not saccade onset)
>>>> Is there a different method I should be using?
>>>>
>>>> I have posted some sample data and the current script (which  
>>>> reads in the
>>>> data and runs preprocessing) to the following urls:
>>>>
>>>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat
>>>> http://greenant.net/temp/EOG_analysis.m
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>> _______________________________________________
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>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> ________________________________________________________
>> Stephan Moratti, PhD
>>
>> see also: http://web.me.com/smoratti/
>>
>> Universidad Complutense de Madrid
>> Facultad de Psicología
>> Departamento de Psicología Básica I
>> Campus de Somosaguas
>> 28223 Pozuelo de Alarcón (Madrid)
>> Spain
>> and
>> Center for Biomedical Technology
>> Laboratory for Cognitive and Computational Neuroscience
>> Parque Científico y Tecnológico de la Universidad Politecnica de  
>> Madrid
>> Campus Montegancedo
>> 28223 Pozuelo de Alarcón (Madrid)
>> Spain
>>
>>
>> email: smoratti at psi.ucm.es
>> Tel.:    +34 679219982
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> ________________________________________________________
>> Stephan Moratti, PhD
>>
>> see also: http://web.me.com/smoratti/
>>
>> Universidad Complutense de Madrid
>> Facultad de Psicología
>> Departamento de Psicología Básica I
>> Campus de Somosaguas
>> 28223 Pozuelo de Alarcón (Madrid)
>> Spain
>> and
>> Center for Biomedical Technology
>> Laboratory for Cognitive and Computational Neuroscience
>> Parque Científico y Tecnológico de la Universidad Politecnica de  
>> Madrid
>> Campus Montegancedo
>> 28223 Pozuelo de Alarcón (Madrid)
>> Spain
>>
>>
>> email: smoratti at psi.ucm.es
>> Tel.:    +34 679219982
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


________________________________________________________
Stephan Moratti, PhD

see also: http://web.me.com/smoratti/

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982


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