[Eeglablist] Problems with Creating Study and running precomputing - preclustering

[Maya Pinacle]

Hi Makoto,


thank you very much for the answer. I tried what you described in your
email. I didn't get the error message then. But the wierd thing is when I
run Build Preclustering Matrix from the Study > PCA Clustering Menu it runs
without no error, however at the end of the whole process there is no any
record of parameters in the Study.preclust structures (erpclusttimes,
specclustfreqs, erspclustfreqs, erspclusttimes), they are all empty is that
normal?

And then when I try to run Cluster Components from the menu with K-means
and choosing 3 cluster for example, I get an error that is saying '' Too
many input arguments (Error occured in function pop_clust() at line 184)
which line calls k-means function actually.

So I am stuck really and do you think is there any link between not having
any record of parameters in the anywhere under Study structure and not
being able to run Cluster Components? And do you think these all again go
down to the STUDY cannot read the data sets properly even though it seems
running the precomputing and preclustering without an error?

For your first question, I have actually 5 condition, for each condition I
try to do seperate network analyisis to see within-condition network using
ICs belongs only to that condition. Do you think this might be a problem as
well? I mean I am not interested in with statistical comparison between the
conditions at this stage, the only thing that I am interested in at the
moment is to see whether is there a network specific to each single
condition.

Thank you very much for any help indeed,

Maya




2016-06-09 3:09 GMT+01:00 Makoto Miyakoshi <mmiyakoshi at ucsd.edu>:

> Dear Maya,
>
> Sorry for the trouble.
>
> > each collected for only one condition
>
> Do you mean there is no within-subject condition?
>
> > ''Warning: ICA ERSP or ITC data files computed with old version of
> EEGLAB for design 1 (and maybe other designs). These files may be corrupted
> and must be recomputed.''
>
> This message has been there for LONG time. It's a false alarm.
>
> > '' Error using eeglab (line 1006)
> Error: ()-indexing must appear last in an index expression.
> You are using the latest version of EEGLAB.
> Warning: STUDY moved since last saved, trying to load data files using
> relative path
> pop_loadset(): loading file C:\Users\tc025847\Desktop\Mitchell Replica
> Experiment Files\EEG only\DATA\3\Category_5_ICAremoved.set ...
> Reading float file 'C:\Users\tc025847\Desktop\Mitchell Replica Experiment
> Files\EEG only\DATA\3\Category_5_ICAremoved.fdt'... ''
>
> I don't know about this error.
> Maybe your folder structure is bad... my guess is that STUDY is trying to
> use relative path but failing. What I would try is that I would move all
> the .set and precompute files into one folder and create another STUDY
> there with exact same data and STUDY.design. In this way, you can skip
> precompute and immediately start from precluster.
>
> Makoto
>
>
> On Tue, Jun 7, 2016 at 3:45 AM, Maya Pinacle <mayapinacle at gmail.com>
> wrote:
>
>> Hi,
>>
>> I have just started using STUDY with EEGLAB, I have data from 10 subjects
>> in different 10 folders, each collected for only one condition and I would
>> like to extract clusters of ICs of those datasets using STUDY. I have
>> already run ICA and Dipfit to extract ICs and corresponding dipoles. When I
>> create a Study with those 10 subject's data and save it to a folder and
>> again want to load it back to the EEGLAB, I always get this warning message
>> in a popup window which says
>>
>>
>> ''Warning: ICA ERSP or ITC data files computed with old version of EEGLAB
>> for design 1 (and maybe other designs). These files may be corrupted and
>> must be recomputed.''
>>
>>
>> and also in the command line there is a warning saying
>>
>> '' Error using eeglab (line 1006)
>> Error: ()-indexing must appear last in an index expression.
>> You are using the latest version of EEGLAB.
>> Warning: STUDY moved since last saved, trying to load data files using
>> relative path
>> pop_loadset(): loading file C:\Users\tc025847\Desktop\Mitchell Replica
>> Experiment Files\EEG only\DATA\3\Category_5_ICAremoved.set ...
>> Reading float file 'C:\Users\tc025847\Desktop\Mitchell Replica Experiment
>> Files\EEG only\DATA\3\Category_5_ICAremoved.fdt'... ''
>> ...
>>
>> This message continues for each single file that I have used to create
>> STUDY. However there is no change of datesets' location at all but STUDY
>> seems struggling to find the datasets. Eventually EEGLAB seems loading the
>> *.study file and I run preclustering on the data, however there is no
>> preclustering parameters are set either.
>>
>>
>> These are the code lines how I run precomputing and preclustering
>>
>> % precomputing
>>  [STUDY ALLEEG] = std_precomp(STUDY, ALLEEG,
>> 'components','erp','on','erpparams',{'rmbase' [-200 1]
>> },'scalp','on','spec','on','specparams',{'specmode' 'fft' 'logtrials'
>> 'off'},'erpim','on','erpimparams',{'nlines' 10 'smoothing'
>> 10},'ersp','on','erspparams',{'cycles' [3 0.5] 'freqs' [3 45] 'alpha' 0.01
>> 'padratio' 1},'itc','on');
>>
>>
>>  % preclustering
>>  [STUDY ALLEEG] = std_preclust(STUDY, ALLEEG, 1,{'spec' 'npca' 5 'norm' 1
>> 'weight' 1 'freqrange' [3 45] },{'erp' 'npca' 5 'norm' 1 'weight' 1
>> 'timewindow' [-500 1000] },{'scalp' 'npca' 5 'norm' 1 'weight' 1 'abso'
>> 1},{'dipoles' 'norm' 1 'weight' 10},{'ersp' 'npca' 5 'freqrange' [3 45]
>> 'timewindow' [-500 1000]  'norm' 1 'weight' 1},{'itc' 'npca' 5 'freqrange'
>> [3 45]  'timewindow' [-500 1000]  'norm' 1 'weight' 1},{'finaldim' 'npca'
>> 5});
>>
>>
>> These codes run smoothly however there is no parameters stored in
>> theStudy.cluster.precluster.preclusterparams and preclusterdata
>>
>>
>> And when I run all these processes on the sample data I got the same
>> error messages and nothing was stored in those Study structures at all.
>>
>>
>> Is there anyone encountered this problem before? Do you have any idea
>> what could be the problem? I would appreciate any help please.
>>
>> Thank you,
>>
>> Maya.
>>
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>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>
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