[Mne_analysis] Error using mne_average_estimates

[dgw]

Hi Kestas,

Perhaps you could describe your specific problem for us, since it is
not the same as the previous one.

D

On Tue, Mar 18, 2014 at 4:10 PM, Kestas Kveraga
<kestas at nmr.mgh.harvard.edu> wrote:
> 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/
>>> >
>>> > _______________________________________________
>>> > Mne_analysis mailing list
>>> > Mne_analysis at nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>> >
>>> >
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>>
>>
>>
>>
>> --
>> Stephen Politzer-Ahles
>> University of Kansas
>> Linguistics Department
>> http://www.linguistics.ku.edu/
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> 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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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>