Average with MNE: Memory Allocation Failed

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1

Hello everyone,

I have a problem to average my data across subjects.
I have 7 files per subject of 750 Mo each and 7 subjects.
I tried mne_process_raw to average my data all together. At around the two
third of the process I have this error message : 'fiff_read_tag: memory
allocation failed'.
I tried to use the MNE matlab toolbox. I averaged my subjects separately and
then try to load the averages in Matlab to average all the subjects together
in matlab. But there also is a problem of memory while loading the data.

Does anybody have an idea of how I could solve this ?

Also, does anybody know how to save the terminal info while using the
mne_process_raw command ? I would like to know how many trials mne averaged
in each category and save it in a file.

Thanks in advance,

Lucie

2009/4/28 Matti Hamalainen <msh at nmr.mgh.harvard.edu>

Hello all,

Thanks to Fran?ois Tadel from USC and John Mosher from Cleveland Clinic,
one major and a few minor bottlenecks were identified in the MNE Matlab
Toolbox. I modified the code on the basis of their findings and, as a
result, the fif file I/O is now much faster. I packaged the improved version
as MNE Matlab 2.6.1 and this new version is now available on the download
web site.

This new package is highly recommended for those of you who use the MNE
Matlab tools.

The Martinos Center public MNE installation has been updated.

Other users need to:

1. Download MNE-dist-matlab-2.6.1-090428065405.tar.gz from the MNE download
web site.

2. Goto the directory *containing* $MNE_ROOT, i.e., $MNE_ROOT/..

3. Say

tar zxvf <where the download is>/MNE-dist-matlab-2.6.1-090428065405.tar.gz

<where the download is> is the path to the directory where you downloaded
the software.

Best,
Matti

  ---------

Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital

msh at nmr.mgh.harvard.edu

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Mne_analysis at nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

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2

Hi Lucie,

See some replies in text.

Hello everyone,

I have a problem to average my data across subjects.
I have 7 files per subject of 750 Mo each and 7 subjects.
I tried mne_process_raw to average my data all together. At around
the two third of the process I have this error message :
'fiff_read_tag: memory allocation failed'.
I tried to use the MNE matlab toolbox. I averaged my subjects
separately and then try to load the averages in Matlab to average
all the subjects together in matlab. But there also is a problem of
memory while loading the data.

Does anybody have an idea of how I could solve this ?

Load them one at a time i.e.
data=fiff_read_evoked('subject1')
for i=2:6)
data2=fiff_read_evoked(['subject' i])
data.evoked=data.evoked+data2.evoked;
end
data.evoked=data.evoked./7;

Also, does anybody know how to save the terminal info while using
the mne_process_raw command ? I would like to know how many trials
mne averaged in each category and save it in a file.

Lucie this is already in both the fif file and in the log file
generated by mne_process_raw.

Thanks in advance,

Lucie

2009/4/28 Matti Hamalainen <msh at nmr.mgh.harvard.edu>

Hello all,

Thanks to Fran?ois Tadel from USC and John Mosher from Cleveland
Clinic, one major and a few minor bottlenecks were identified in
the MNE Matlab Toolbox. I modified the code on the basis of their
findings and, as a result, the fif file I/O is now much faster. I
packaged the improved version as MNE Matlab 2.6.1 and this new
version is now available on the download web site.

This new package is highly recommended for those of you who use the
MNE Matlab tools.

The Martinos Center public MNE installation has been updated.

Other users need to:

1. Download MNE-dist-matlab-2.6.1-090428065405.tar.gz from the MNE
download web site.

2. Goto the directory *containing* $MNE_ROOT, i.e., $MNE_ROOT/..

3. Say

tar zxvf <where the download is>/MNE-dist-
matlab-2.6.1-090428065405.tar.gz

<where the download is> is the path to the directory where you
downloaded the software.

Best,
Matti

---------

Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital

msh at nmr.mgh.harvard.edu

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

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