[Mne_analysis] Error using mne_average_estimates

Hari Bharadwaj hari at nmr.mgh.harvard.edu
Tue Mar 18 17:36:34 EDT 2014
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Hi Kestas,
   Just in case: One mistake that I have run into the past when resampling
the STC is that I would be missing the end point samples when
specifying tmin, tmax, tstep. For instance, the last STC sample would
be something like 1.995s for a different data set epoched with the same
code, whereas tmax is set to 2000 ms.

Hari


On Tue, March 18, 2014 4:10 pm, Kestas Kveraga 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
>
>
>
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis


-- 
Hari Bharadwaj
PhD Candidate, Biomedical Engineering,
Boston University
677 Beacon St.,
Boston, MA 02215

Martinos Center for Biomedical Imaging,
Massachusetts General Hospital
149 Thirteenth Street,
Charlestown, MA 02129

hari at nmr.mgh.harvard.edu
Ph: 734-883-5954





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