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

[Nikola Vukovic]

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
>
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