[Eeglablist] run AMICA

Tue May 8 13:06:04 PDT 2018

Hi Gian,

I got similar errors. The first thing I checked was that MPICH is installed
(mpich2-1.4.1p1-win-x86-64 worked for me). Second, there should be no
spaces in the path and filename of your dataset and the out directory for
AMICA.

When processing all participants data, I usually keep the path for amicaout
to a temporary folder on the desktop and then move it to the
intended/required folder using MATLAB's movefile function.

I hope this helps.

Regards,

M. Samran Navid.

On Tue, May 8, 2018 at 9:00 PM, <eeglablist-request at sccn.ucsd.edu> wrote:

> Send eeglablist mailing list submissions to
>         eeglablist at sccn.ucsd.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://sccn.ucsd.edu/mailman/listinfo/eeglablist
> or, via email, send a message with subject or body 'help' to
>         eeglablist-request at sccn.ucsd.edu
>
> You can reach the person managing the list at
>         eeglablist-owner at sccn.ucsd.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of eeglablist digest..."
>
> Today's Topics:
>
>    1. run AMICA (Gian Marco Duma)
>    2. NaN in AMICA (Tyler Grummett)
>
>
> ---------- Forwarded message ----------
> From: Gian Marco Duma <gmduma90 at gmail.com>
> To: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Cc:
> Bcc:
> Date: Mon, 7 May 2018 20:46:41 +0200
> Subject: [Eeglablist] run AMICA
> Hi everybody,
> I'm actually trying to run AMICA but I'm having some problems in doing it.
> I dowloaded AMICA 1.5 and I putted it into plug-in folder of EEGLAB. When I
> open EEGLAB I correctly find AMICA in the tools. I loaded a .set file and I
> tryed to run AMICA without changing the default parameters, but I had some
> errors in Matlab:
>
>
> No datfile field found in EEG structure. Will write temp file.
> Writing data file: C:\Users\Utente\Desktop\eeglab14_1_0b\tmpdata81472.fdt
> Sottodirectory o file C:\Users\Utente\Desktop\SPCN_
> 2017\Dati.set\SPCN_ICA_pruned\amicaout\ già esistente.
> No gm present, setting num_models to 1
> No W present, exiting
> Reference to non-existent field 'W'.
>
> Error in runamica15 (line 873)
>     weights = mods.W(:,:,1);
>
> Error in pop_runamica (line 242)
>     [W,S,mods] = runamica15(EEG.data(:,:),arglist{:});
>
> Have you any suggestions about how to solve these errors?
> Thanks
> Gian Marco
>
>
> ---------- Forwarded message ----------
> From: Tyler Grummett <tyler.grummett at flinders.edu.au>
> To: EEGLABLIST <eeglablist at sccn.ucsd.edu>
> Cc:
> Bcc:
> Date: Tue, 8 May 2018 03:12:51 +0000
> Subject: [Eeglablist] NaN in AMICA
>
> Dear EEGLABers (particularly Jason Palmer)
>
>
> Ive been using EEGLAB and AMICA for many years now and theres been an
> issue I've been meaning to ask about for a while now. Sometimes when I run
> an AMICA, the 'LL' and 'nd' in the final iteration are NaNs. For example
> (last couple lines of output):
>
>
> ...
>
>  iter  3993 lrate =  0.0000004768 LL =   0.2151813642 nd =  0.0066193118,
> D =   0.11548E+01  0.11548E+01  ( 44.53 s, 198.0 h)
>  iter  3994 lrate =  0.0000004768 LL =   0.2151813668 nd =  0.0066193124,
> D =   0.11548E+01  0.11548E+01  ( 44.42 s, 197.5 h)
>  iter  3995 lrate =  0.0000004768 LL =   0.2151813695 nd =  0.0066193130,
> D =   0.11548E+01  0.11548E+01  ( 44.42 s, 197.5 h)
>  iter  3996 lrate =  0.0000004768 LL =   0.2151813720 nd =  0.0066193133,
> D =   0.11548E+01  0.11548E+01  ( 44.56 s, 198.1 h)
>  iter  3997 lrate =  0.0000004768 LL =   0.2151813746 nd =  0.0066193139,
> D =   0.11548E+01  0.11548E+01  ( 44.27 s, 196.8 h)
>  iter  3998 lrate =  0.0000004768 LL =   0.2151813771 nd =  0.0066193143,
> D =   0.11548E+01  0.11548E+01  ( 44.55 s, 198.0 h)
>  iter  3999 lrate =  0.0000004768 LL =   0.2151813797 nd =  0.0066193143,
> D =   0.11548E+01  0.11548E+01  ( 44.49 s, 197.7 h)
>  iter  4000 lrate =  0.0000004768 LL =   0.2151813823 nd =  0.0066193152,
> D =   0.11548E+01  0.11548E+01  ( 44.05 s, 195.8 h)
>  iter  4001 lrate =  0.0000004768 LL =   0.2151813824 nd =  0.0066193255,
> D =   0.11548E+01  0.11548E+01  ( 48.06 s, 213.6 h)
>  iter  4002 lrate =  0.0000004768 LL =   0.2151813847 nd =  0.0066193309,
> D =   0.11548E+01  0.11548E+01  ( 44.39 s, 197.3 h)
>  iter  4003 lrate =  0.0000004768 LL =   0.2151813871 nd =  0.0066193324,
> D =   0.11548E+01  0.11548E+01  ( 44.35 s, 197.1 h)
>  iter  4004 lrate =  0.0000004768 LL =   0.2151813892 nd =  0.0066193335,
> D =   0.11548E+01  0.11548E+01  ( 44.49 s, 197.7 h)
>  iter  4005 lrate =  0.0000004768 LL =   0.2151813914 nd =  0.0066193340,
> D =   0.11548E+01  0.11548E+01  ( 44.62 s, 198.2 h)
>  iter  4006 lrate =  0.0000004768 LL =            NaN nd =           NaN,
> D =   0.11548E+01  0.11548E+01  ( 44.28 s, 196.7 h)
>  Got NaN! Exiting ...
> ... done. Execution time: -10.23 h
>
> Since first noticing this till now, I have code that checks the output for
> this issue and reruns the AMICA. A lot of the time it will eventually and
> properly end with the learning rate not decreasing by 1e-9 for five
> iterations (I think thats what it is). Ive checked the data, it seems fine.
>
>
> I guess what I am asking is: "Is this an issue?" or am I incorrectly
> classifying it as an issue. If it is an issue, Im wondering why it doesnt
> reset itself.
>
>
> Kind regards,
>
> Tyler
>
>
> *************************
>
> *Tyler Grummett ( BBSc, BSc(Hons I))*
> *PhD Candidate*
> *Brain Signals Laboratory*
> *Multimodal Recording Facility*
> *Flinders University Tonsley Building*
> *Rm 4.17*
> *Ext 19573*
>
> _______________________________________________
> eeglablist mailing list eeglablist at sccn.ucsd.edu
> Eeglablist page: http://www.sccn.ucsd.edu/eeglab/eeglabmail.html
> To unsubscribe, send an empty email to eeglablist-unsub at sccn.ucsd.edu
> To switch to non-digest mode, send an empty email to
> eeglablist-nodigest at sccn.ucsd.edu
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://sccn.ucsd.edu/pipermail/eeglablist/attachments/20180508/043ca334/attachment.html>