Are there some publicly available functional labels (for example, for
visual zones - V1, V2, etc) for standard brain?
I need to do some analysis of brain activity, separately for each of those
zones. Obviously, I could create such labels by hand, but the result would
be probably messy and imprecise.
Could there be something wrong with my freesurfer reconstruction?
2012/10/17 Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
Hi,
V1 and V2 labels are given by the freesurfer reconstructions.
look in the "label? folder of the freesurfer recon.
HTH
Alex
> Hello!
>
> Are there some publicly available functional labels (for example, for
visual
> zones - V1, V2, etc) for standard brain?
>
> I need to do some analysis of brain activity, separately for each of
those
> zones. Obviously, I could create such labels by hand, but the result
would
> be probably messy and imprecise.
>
> Best wishes,
> Platon Pronko
>
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Yes, I do visualize those annotations using mne_analyze. Sadly, those
annotations contain only anatomical labels (G_precentral, S_occipital_ant,
etc.), but no functional ones.
2012/10/17 Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
hi,
you can visualize annotations (they are many labels in one file) with
tksurfer, pysurfer or mne_analyze
to split the annot into labels use:
mne_annot2labels
HTH
A
> Thanks for you reply!
>
> I looked in that folder - it only contains these files:
>
> aparc.annot.a2009s.ctab
> aparc.annot.ctab
> lh.aparc.a2009s.annot
> lh.aparc.annot
> lh.cortex.label
> rh.aparc.a2009s.annot
> rh.aparc.annot
> rh.cortex.label
>
> Could there be something wrong with my freesurfer reconstruction?
>
> 2012/10/17 Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
>>
>> Hi,
>>
>> V1 and V2 labels are given by the freesurfer reconstructions.
>>
>> look in the "label? folder of the freesurfer recon.
>>
>> HTH
>>
>> Alex
>>
>> > Hello!
>> >
>> > Are there some publicly available functional labels (for example, for
>> > visual
>> > zones - V1, V2, etc) for standard brain?
>> >
>> > I need to do some analysis of brain activity, separately for each of
>> > those
>> > zones. Obviously, I could create such labels by hand, but the result
>> > would
>> > be probably messy and imprecise.
>> >
>> > Best wishes,
>> > Platon Pronko
>> >
>> > _______________________________________________
>> > 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.
>> >
>
>
2012/10/17 Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
hi
you need lh.BA.annot and rh.BA.annot to have V1 and V2 labels.
A
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Docs for recon-all state that "-autorecon-all" is the same as "-all", so
that doesn't seem to be a problem.
2012/10/17 Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
> And how can I obtain those files (lh.BA.annot)?
you should have it if you used :
recon-all -all ?
at least I have it for all my subjects
Alex
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Yeah, it must be some oddity with Freesurfer. We've been doing recon --all
with Freesurfer x86_64 5.1.0 and our subjects have lh.BA.annot. If you
figure it out, let us know!