[Mne_analysis] Issues generating functional labels for RH

[Natalie Klein]

My guess is stc_to_label doesn't like 'connected=True' when you have
vertices in both hemispheres but I have not looked at the source code. You
could try 'connected=False' which should return labels in each hemisphere
according to the documentation. Either that, or try to figure out why your
parcellation labels are resulting in vertices in both hemispheres and
change that. (The ROIs I used to restrict the stc were hand drawn in
Freesurfer, so when I use 'stc.in_label(label)', I only get vertices in one
hemisphere; 'stc.vertices' returns a list in which one of the arrays is
empty.)

On Fri, Mar 4, 2016 at 9:57 AM, Cushing, Cody <CCUSHING1 at mgh.harvard.edu>
wrote:

> Hm, well the problem must be with me somewhere then.  If I run the code
> for a right hemi parc, I get:
>
> In [50]: stc_mean.vertices
> Out[50]:
> [array([    12,     68,     76, ..., 132204, 132241, 132257]),
>  array([     7,     38,     43, ..., 134417, 134419, 134449])]
>
> If I run it on the left hemisphere, I get the exact same thing.  Do those
> two arrays represent vertices for each hemisphere?  Or is that telling me
> its looking at the same vertices (only in the lh) when looking for rh
> activation?
>
> ------------------------------
> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu [
> mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Natalie Klein [
> neklein at andrew.cmu.edu]
> *Sent:* Friday, March 04, 2016 9:46 AM
> *To:* Discussion and support forum for the users of MNE Software
> *Subject:* Re: [Mne_analysis] Issues generating functional labels for RH
>
> I've recently run my own code based on this example and it works for both
> hemispheres. Just guessing here, but what does stc_mean.vertices look like?
> Does it have vertices in the correct hemisphere?
>
> On Fri, Mar 4, 2016 at 9:37 AM, Cushing, Cody <CCUSHING1 at mgh.harvard.edu>
> wrote:
>
>> Hi all,
>>
>> I have been attempting to generate functional labels from source
>> estimates for a data set as outlined here:
>> https://martinos.org/mne/stable/auto_examples/inverse/plot_label_from_stc.html#sphx-glr-auto-examples-inverse-plot-label-from-stc-py
>>
>> This works beautifully for all the left hemisphere parcellations I try,
>> but whenever I try a right hemisphere counter-part, the list of func_labels
>> return empty, causing the below indexing error:
>>
>>
>> ---------------------------------------------------------------------------
>> IndexError                                Traceback (most recent call
>> last)
>> [] in <module>()
>>      57
>>      58 # take first as func_labels are ordered based on maximum values
>> in stc
>> ---> 59 func_label = func_labels[0]
>>      60
>>      61
>>
>> IndexError: list index out of range
>>
>> I have tried a couple of subjects and a variety of different parc
>> labels.  I have played with different time windows and eventually just
>> opened it up to the whole trial (1s).  Every lh parc label works fine, but
>> not a single rh parc I have tried returns any functional labels from this
>> line of code:
>>
>> func_labels,_ = mne.stc_to_label(stc_mean_label, src=src, smooth=True,
>>                                   subjects_dir=subjects_dir,
>> connected=True)
>>
>> There is data in stc_mean_label.data.  I do not believe it could be due
>> to a lack of right hemisphere activation because looking at the dSPM
>> activations in mne_analyze shows just as much if not more activity in the
>> right hemisphere for the parcellation pairs I've looked at (e.g.
>> fusiform-rh and fusiform-lh).  The label is read fine (from the proper
>> hemisphere), so I'm not quite sure what the problem is.  Is it possible
>> that the empty return is a result of the module only looking in left
>> hemisphere source space (where obviously no right hemisphere activation
>> will be found)?
>>
>> Any help is greatly appreciated and I'm happy to supply whatever
>> additional information.  The only changes I have made from the source code
>> are supplying in my own paths for my personal data, but I am happy to
>> provide my code upon request.
>>
>> Cheers,
>> Cody
>>
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