[Eeglablist] Error while precomputing STUDY: NaN values in cluster.sets

Makoto Miyakoshi mmiyakoshi at ucsd.edu
Tue Dec 1 14:39:51 PST 2015


Dear Nikola,

It's just my guess, but it could be related to folder permission status,
Matlab configuration (default Matlab home folder etc), etc... you might
want to file it to EEGLAB bugzilla if you think it's not specific to your
environment.

Makoto

On Tue, Dec 1, 2015 at 1:05 PM, Nikola Vukovic <vukovicnikola at gmail.com>
wrote:

> It's a strange bug.. When I typed "which -all eeg_options" it returned
> only one location, but now I went and manually found the second
> eeg_option.m file. I tried changing some settings from the GUI, and they
> definitely end up reflected in this file...
>
> Nikola
>
> On Tue, Dec 1, 2015 at 9:57 PM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> wrote:
>
>> Which means your system failed to create the eeg_option. The one that
>> comes with EEGLAB is like a template. Currently, your EEGLAB is running
>> without writable eeg_option!
>>
>> Makoto
>>
>> On Tue, Dec 1, 2015 at 12:52 PM, Nikola Vukovic <vukovicnikola at gmail.com>
>> wrote:
>>
>>> Hmm, so there should be two option files then? In my case "which -all
>>> eeg_options" only returns one
>>> line: /Applications/EEGLAB/eeglab13.5.4b/functions/adminfunc/eeg_options.m
>>>
>>>
>>> On Tue, Dec 1, 2015 at 9:46 PM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
>>> wrote:
>>>
>>>> Dear Nikokla,
>>>>
>>>> Try 'which -all eeg_options'. What does it say? I show mine below as an
>>>> example of good case.
>>>>
>>>> >> which -all eeg_options
>>>> /home/makoto/eeg_options.m
>>>> /data/projects/makoto/Tools/eeglab/functions/adminfunc/eeg_options.m  %
>>>> Shadowed
>>>>
>>>> Makoto
>>>>
>>>> On Tue, Dec 1, 2015 at 12:37 PM, Nikola Vukovic <
>>>> vukovicnikola at gmail.com> wrote:
>>>>
>>>>> Hi Makoto,
>>>>>
>>>>> In the options pop up, precomputing ICA is checked correctly, and I
>>>>> think also in the option file. Here's what's inside:
>>>>>
>>>>> % eeg_options() - eeglab option script
>>>>> %
>>>>> % Note: DO NOT EDIT, instead use pop_editoptions() or the menu
>>>>> %       /File/Maximize memory in EEGLAB gui
>>>>>
>>>>> % STUDY and file options (set these checkboxes if you intend to work
>>>>> with studies)
>>>>> option_storedisk = 1 ; % If set, keep at most one dataset in memory.
>>>>> This allows processing hundreds of datasets within studies.
>>>>> option_savetwofiles = 1 ; % If set, save not one but two files for
>>>>> each dataset (header and data). This allows faster data loading in studies.
>>>>> option_saveversion6 = 1 ; % If set, write Matlab files in Matlab v6.5
>>>>> (max compatibility). If not, write files in Matlab v7.3 (larger than 2Gb).
>>>>> % Memory options
>>>>> option_single = 1 ; % If set, use single precision under Matlab 7.x.
>>>>> This saves RAM but can lead to rare numerical imprecisions.
>>>>> option_memmapdata = 0 ; % If set, use memory mapped array under Matlab
>>>>> 7.x. This may slow down some computation (beta).
>>>>> option_eegobject = 0 ; % If set, use the EEGLAB EEG object instead of
>>>>> the standard EEG structure (beta).
>>>>> % ICA options
>>>>> option_computeica = 1 ; % If set, precompute ICA activations. This
>>>>> requires more RAM but allows faster plotting of component activations.
>>>>> option_scaleicarms = 1 ; % If set, scale ICA component activities to
>>>>> RMS (Root Mean Square) in microvolt (recommended).
>>>>> % Folder options
>>>>> option_rememberfolder = 1 ; % If set, when browsing to open a new
>>>>> dataset assume the folder/directory of previous dataset.
>>>>> % Toolbox options
>>>>> option_donotusetoolboxes = 0 ; % If set, do not use Matlab additional
>>>>> toolboxes functions even if they are present (need to restart EEGLAB).
>>>>> % EEGLAB connectivity and support
>>>>> option_checkversion = 1 ; % If set, check for new version of EEGLAB at
>>>>> startup.
>>>>> option_chat = 0 ; % If set, enable EEGLAB chat - currently UCSD only -
>>>>> restart EEGLAB after changing that option.
>>>>>
>>>>>
>>>>> Nikola
>>>>>
>>>>> On Tue, Dec 1, 2015 at 9:25 PM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
>>>>> wrote:
>>>>>
>>>>>> Dear Nikola,
>>>>>>
>>>>>> I've seen this. In my case at least, it was because EEGLAB's default
>>>>>> set up file was not correctly figured out, which prevented EEGLAB from
>>>>>> creating EEG.icaact etc (do you remember that there are some items in
>>>>>> 'memory and other options' that determines what to do with computed ica
>>>>>> data... maybe related to that). After fixing the default parameter file, it
>>>>>> start to work normally.
>>>>>>
>>>>>> I don't know if this is also the case for you, but just in case
>>>>>> please check it out.
>>>>>>
>>>>>> Makoto
>>>>>>
>>>>>> On Mon, Nov 23, 2015 at 3:33 PM, Nikola Vukovic <
>>>>>> vukovicnikola at gmail.com> wrote:
>>>>>>
>>>>>>> Dear EEGLAB list
>>>>>>>
>>>>>>> I would be very grateful is someone could help me out with an error
>>>>>>> I've been getting. When I try to precluster components in a given STUDY (it
>>>>>>> happens for several study files), I get the following error:
>>>>>>>
>>>>>>> FOR CLUSTERING, YOU MAY ONLY USE DIPOLE OR SCALP MAP CLUSTERING. This is
>>>>>>> because some datasets do not have ICA pairs. Look for NaN values in
>>>>>>> STUDY.cluster(1).sets which indicate missing datasets. Each column in this
>>>>>>> array indicate datasets with common ICA decompositions.
>>>>>>>
>>>>>>> Looking inside the cluster(1).sets, I can indeed find some NaN fields, suggesting not all files have associated ICA decomposition data. This, however, is puzzling because I made sure to do ICA on each subject's dataset *before* epoching, meaning that all sets for individual conditions share the same weights for a subject. After getting this error I even tried to copy the weights (EEG.icawinv + EEG.icasphere + EEG.icaweights + EEG.icachansind) from the unepoched set to all the epoched ones.
>>>>>>>
>>>>>>> Did anyone have this error too, and how could it be solved?
>>>>>>>
>>>>>>> Thanks for any help,
>>>>>>>
>>>>>>> Nikola
>>>>>>>
>>>>>>>
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>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Makoto Miyakoshi
>>>>>> Swartz Center for Computational Neuroscience
>>>>>> Institute for Neural Computation, University of California San Diego
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Makoto Miyakoshi
>>>> Swartz Center for Computational Neuroscience
>>>> Institute for Neural Computation, University of California San Diego
>>>>
>>>
>>>
>>
>>
>> --
>> Makoto Miyakoshi
>> Swartz Center for Computational Neuroscience
>> Institute for Neural Computation, University of California San Diego
>>
>
>


-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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