[Mne_analysis] Error using mne_average_estimates

[Kestas Kveraga]

Hi Steve,
but I'm running a network version of MNE at MGH, so that should not be a problem?
thanks,
Kestas

On Mar 18, 2014, at 2:42 PM, Stephen Politzer-Ahles wrote:

> Hi Kestas,
> 
> In my case, the problem was solved by adding libgfortran.so.1 to my library; the rest of this discussion must have been off-list or ended up in another thread. I believe somewhere on the list, someone sent me (via attachment) a copy of this file which I could download and put in  /usr/lib64/, which fixed the issue.
> 
> Best,
> Steve
> 
> 
> 
> Stephen Politzer-Ahles
> New York University, Abu Dhabi
> Neuroscience of Language Lab
> http://www.nyu.edu/projects/politzer-ahles/
> 
> 
> On Tue, Mar 18, 2014 at 9:38 PM, Kestas Kveraga <kestas at nmr.mgh.harvard.edu> wrote:
> Hi,
> I was wondering whether this issue was solved, as I am having it as well (despite previously using identically scripted commands and .desc files to successfully make average stc files on a different data set).
> The error doesn't provide much info - after compiling the individual stc files, after 'Temporal resampling...' the first subject stc file, it simply says [failed]. 
> Any ideas?
> 
> Thanks,
> Kestas
> 
> 
> On Mar 31, 2012, at 6:44 AM, Stephen Politzer-Ahles wrote:
> 
>> Hi Alex,
>> 
>> Thank you. Here are links to two of my stc files and to the mne_average_estimates description file:
>> http://dl.dropbox.com/u/9929284/AL023_ave-rh.stc
>> http://dl.dropbox.com/u/9929284/AL023_ave-lh.stc
>> http://dl.dropbox.com/u/9929284/stcdescrip
>> 
>> I made the stc files using the following command line:
>> 
>> mne_make_movie --subject $SUBJECT --meas $SAMPLE/MEG/$SUBJECT/$SUBJECT"_ave.fif" --inv $SAMPLE/MEG/$SUBJECT/$SUBJECT"_ave-7-meg-inv.fif" --morph average --smooth 5 --stc $SAMPLE/MEG/$SUBJECT"_ave"
>> 
>> (My directory structure is, within $SAMPLE I have a /subjects folder with the MRI data and an /MEG folder with the MEG data.) I didn't use the --bmin and --bmax options because I already did baseline correction when I averaged the MEG data.
>> 
>> After creating stc files like that for every subject, I ran 
>> 
>> mne_average_estimates --desc stcdescrip
>> 
>> using the attached description file.
>> 
>> Best,
>> Steve
>> 
>> On Sat, Mar 31, 2012 at 3:47 AM, Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu> wrote:
>> hi Steve,
>> 
>> In case you have not solved your problem yet, can you share a couple
>> of stc files that cause
>> the problem and give me the exact command line you typed?
>> 
>> Alex
>> 
>> On Fri, Mar 30, 2012 at 8:30 PM, Stephen Politzer-Ahles
>> <politzerahless at gmail.com> wrote:
>> > Hello,
>> >
>> > I'm encountering an error running mne_average_estimates. The program
>> > successfully loads all my stc files and sets up the time scale, but then I
>> > get:
>> >
>> > Temporal resampling...
>> > /<path to my data>/subj001_ave-lh.stc .. LH .. [failed]
>> >
>> > Before running mne_average_estimates, I had first created an average brain
>> > in Freesurfer (make_average_subject), then created morph maps from each
>> > subject to the average brain (mne_make_morph_maps --from <subject> --to
>> > average), then for each subject did current estimates using mne_make_movie
>> > with "--morph average" specified, so for each subject I have both
>> > <subject>-lh.stc. and <subject>-rh.stc. For mne_average_estimates, my
>> > description file looks like this:
>> >
>> > stc /<path_to_my_data>/subj001_ave-lh.stc
>> > stc /<path_to_my_data>/subj001_ave-rh.stc
>> > stc /<path_to_my_data>/subj002_ave-lh.stc
>> > stc /<path_to_my_data>/subj002_ave-rh.stc
>> > stc /<path_to_my_data>/subj003_ave-lh.stc
>> > ...
>> > deststc /<path_to_my_data>/averagestc
>> >
>> > (I also tried the same thing but without including the "-lh.stc" and
>> > "-rh.stc" in my description file, but I got the same error.)
>> >
>> > Any suggestions or guidance would be greatly appreciated. Thank you very
>> > much!
>> > Steve Politzer-Ahles
>> >
>> > --
>> > Stephen Politzer-Ahles
>> > University of Kansas
>> > Linguistics Department
>> > http://www.linguistics.ku.edu/
>> >
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>> >
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>> 
>> 
>> 
>> -- 
>> Stephen Politzer-Ahles
>> University of Kansas
>> Linguistics Department
>> http://www.linguistics.ku.edu/
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> 
> Kestas Kveraga, Ph.D.
> Instructor in Radiology/Neuroscience
> Martinos Center for Biomedical Imaging
> MGH-Harvard Medical School
> 
> 
> 
> 
> 
> 

Kestas Kveraga, Ph.D.
Instructor in Radiology/Neuroscience
Martinos Center for Biomedical Imaging
MGH-Harvard Medical School





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