[FieldTrip] Problems with Neuromag Data after SSS

Mon Jun 20 00:04:46 CEST 2011

p.s. If this is the problem, try copying using scp from the mac command line, using Terminal - this has always worked for me ok. The files are big endian but this shouldn't be affected by copying to a mac.

Laurence

On 19 Jun 2011, at 20:08, Vladimir Litvak <v.litvak at ion.ucl.ac.uk> wrote:

> 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
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>> 
>> ________________________________________________________
>> 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
>> 
> 
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