[Mne_analysis] Error using mne_average_estimates

Kestas Kveraga kestas at nmr.mgh.harvard.edu
Wed Mar 19 15:48:41 EDT 2014
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It works now: it turned out to be tmin - it was different in the .desc by 0.035 s from the .ave parameters. It's a bit strange as a difference of 0.03 s previously  did not cause a problem.
Thanks for your suggestions!

On Mar 19, 2014, at 1:17 PM, dgw wrote:

> They definitely could be the problem. I would try that first
> 
> On Wed, Mar 19, 2014 at 11:38 AM, Kestas Kveraga
> <kestas at nmr.mgh.harvard.edu> wrote:
>> 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/
>> 
>> 
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>> 
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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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>> 
>> Mne_analysis mailing list
>> 
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>> 
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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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>> 
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>> 
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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
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>> 
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>> Mne_analysis mailing list
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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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>> Mne_analysis mailing list
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>> The information in this e-mail is intended only for the person to whom it is
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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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