[Mne_analysis] Error using mne_average_estimates

Wed Mar 19 11:38:09 EDT 2014

Hi Dan,
I'm running mne_average_estimates --desc [descfileaname] 
which lists individual stc files morphed to a single subject (I've used fsaverage and one of the subjects in the study to morph to).
The individual stc files are fine and display expected activity displayed on the surface to which they were morphed. 
As I said before:
>>> 
>>> 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].

the stc files were made with timing parameters - tmin 0 --tmax 500 (or --tmax 1000) --tstep 10 (or 5) --smooth 6

Could those timing parameters be a problem as Hari suggested? Or something else?
thanks,
Kestas

On Mar 19, 2014, at 11:07 AM, dgw wrote:

> 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
>>>>> 
>>>>> 
>>>>> 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
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>>>>> error
>>>>> but does not contain patient information, please contact the sender and
>>>>> properly
>>>>> dispose of the e-mail.
>>>>> 
>>> 
>>> 
>>> 
>>> 
>>> --
>>> 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
>> 
>> 
>> 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.
>> 
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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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