[Mne_analysis] Error using mne_average_estimates

Wed Mar 19 11:25:19 EDT 2014

Hi Hari,
thank you for your suggestion, I will try to tinker with the timing parameters and report back.
Kestas

On Mar 18, 2014, at 5:36 PM, Hari Bharadwaj wrote:

> 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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> Mne_analysis at nmr.mgh.harvard.edu
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> 
> 

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

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