[Mne_analysis] Error using mne_average_estimates

Wed Mar 19 13:17:04 EDT 2014

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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>
> --
>
> Stephen Politzer-Ahles
>
> University of Kansas
>
> Linguistics Department
>
> http://www.linguistics.ku.edu/
>
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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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>
> 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
>
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>
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>
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>
> properly
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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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