[Mne_analysis] Mne_analysis Digest, Vol 75, Issue 11

Eric Larson larson.eric.d at gmail.com
Fri Apr 11 13:40:07 EDT 2014
Search archives: 
Hey Kam,

It looks like your `stc` somehow has (many) vertices that are not in the
source space. It also looks like that STC has 10242 vertices per
hemisphere, consistent with an ico-5 source space, while the `src` you sent
has 4098 vertices per hemisphere, consistent with an oct-6 source space.
Did you perhaps morph the data to fsaverage ico-5?

I'm opening a PR for mne-python to catch this and throw a better error.

Eric



On Wed, Apr 9, 2014 at 4:14 PM, Kambiz Tavabi <ktavabi at uw.edu> wrote:

> Hi Alex,
> I was not able to reproduce this with the MNE sample data. Please find the
> data files (stc and src) from my study that caused the problem here (
> https://www.dropbox.com/sh/qddmd9vr8rg7hw8/00drNDyuqW). Thanks in
> advance.
>
> Kam
>
> ------------------------------------------------------------
> Kambiz Tavabi PhD
> Institute for Learning & Brain Sciences
> 1715 Columbia Road N
> Portage Bay Building
> Box 357988
> University of Washington
> Seattle, WA 98195-7988
> Tel: 206-685-6173
> ------------------------------------------------------------
>
>
> On Wed, Apr 9, 2014 at 9:00 AM, <mne_analysis-request at nmr.mgh.harvard.edu>wrote:
>
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>>    1. MNEpy stc to label (Kambiz Tavabi)
>>    2. Re: MNEpy stc to label (Alexandre Gramfort)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 8 Apr 2014 12:10:29 -0700
>> From: Kambiz Tavabi <ktavabi at uw.edu>
>> Subject: [Mne_analysis] MNEpy stc to label
>> To: "<Mne_analysis at nmr.mgh.harvard.edu>"
>>         <mne_analysis at nmr.mgh.harvard.edu>
>> Message-ID:
>>         <CACGoKCkGTLTnZ+pi8_T2QU0A=
>> HQjU7_LuQFvc+3JoV3EkoT1PQ at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi all,
>> I am trying to use `mne.stc_to_label` to generate the freesurfer label for
>> connected non-zero vertices. When I pass the `connected=True` argument I
>> receive an index error i.e., "index 4098 is out of bounds for axis 0 with
>> size 4098" at ln 667 of label.py. I am using an oct-6 surface source space
>> with c. 10000 vertices of which 4098 are in use.
>>
>> However, when I pass `connected=False` the list of labels is returned. Can
>> someone tell me why this occurs? and how to get the list of connected
>> labels?
>>
>> regards,
>> Kam
>>
>>
>> ------------------------------------------------------------
>> Kambiz Tavabi PhD
>> Institute for Learning & Brain Sciences
>> 1715 Columbia Road N
>> Portage Bay Building
>> Box 357988
>> University of Washington
>> Seattle, WA 98195-7988
>> Tel: 206-685-6173
>> ------------------------------------------------------------
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>> ------------------------------
>>
>> Message: 2
>> Date: Wed, 9 Apr 2014 08:29:33 +0200
>> From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
>> Subject: Re: [Mne_analysis] MNEpy stc to label
>> To: Discussion and support forum for the users of MNE Software
>>         <mne_analysis at nmr.mgh.harvard.edu>
>> Message-ID:
>>         <
>> CADeotZoWG994W6B1nGZWn6Aq3A2wW6_HnO6x3K7W6V0XtiGGTQ at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> hi Kam,
>>
>> can you reproduce this on the sample dataset?
>>
>> if not can you share a minimum set of files to reproduce the problem?
>>
>> Alex
>>
>>
>> On Tue, Apr 8, 2014 at 9:10 PM, Kambiz Tavabi <ktavabi at uw.edu> wrote:
>> > Hi all,
>> > I am trying to use `mne.stc_to_label` to generate the freesurfer label
>> for
>> > connected non-zero vertices. When I pass the `connected=True` argument I
>> > receive an index error i.e., "index 4098 is out of bounds for axis 0
>> with
>> > size 4098" at ln 667 of label.py. I am using an oct-6 surface source
>> space
>> > with c. 10000 vertices of which 4098 are in use.
>> >
>> > However, when I pass `connected=False` the list of labels is returned.
>> Can
>> > someone tell me why this occurs? and how to get the list of connected
>> > labels?
>> >
>> > regards,
>> > Kam
>> >
>> >
>> > ------------------------------------------------------------
>> > Kambiz Tavabi PhD
>> > Institute for Learning & Brain Sciences
>> > 1715 Columbia Road N
>> > Portage Bay Building
>> > Box 357988
>> > University of Washington
>> > Seattle, WA 98195-7988
>> > Tel: 206-685-6173
>> > ------------------------------------------------------------
>> >
>> > _______________________________________________
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