[Mne_analysis] plot_label_from_stc

[Elisabeth Fonteneau]

Hi Sheraz,
Thanks for your quick answer
I already checked for this directory and file (+
'/fsaverage/bem/fsaverage-ico-5-src.fif')
unfortunately I do not have the directory "bem" in my Average directory
(only label/mri/surf/)
I am reanalysing some old data and I used older version of mne & FreeSurfer
(mne_ version 2.7.3 and freesurfer 4.3.0)
With the command make_average_subject --subjects <list of subjects>
Is there a way or command to create this bem directory and files?
Elisabeth


__________________________________________________________

Dr Elisabeth Fonteneau
Department of Psychology
University of Cambridge
Downing Street, Cambridge CB2 3EB, UK
Email: ef309 at cam.ac.uk
Web: www.neurolex.psychol.cam.ac.uk/directory/ef309 at cam.ac.uk




-----Original Message-----
From: mne_analysis-bounces at nmr.mgh.harvard.edu
[mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of Sheraz Khan,
PhD
Sent: 08 February 2017 20:39
To: Discussion and support forum for the users of MNE Software
Cc: mne_analysis at nmr.mgh.harvard.edu
Subject: Re: [Mne_analysis] plot_label_from_stc

if its fsaverage, you are morphed to for averaging

# select morph grade
src_fsaverage_fname = subjects_dir +
'/fsaverage/bem/fsaverage-ico-5-src.fif'

src_fsaverage = mne.read_source_spaces(src_fsaverage_fname)

func_labels= mne.stc_to_label(stc_mean_label, src_fsaverage, smooth=True,
connected=True)[0]



> Hello MNE experts,
>
> I have a question for creating a Label from a functional STC file
>
>
>
> I found the script plot_label_from_stc.py which is great!
>
>
>
> However when I use the function mne.stc_to_label I am running into a 
> problem
>
>
>
>
> My STC file is an average and morph file and I read it via the command 
> mne_read_source_estimate.
>
> I don't have the source space and I am forced to save the label as 
> unconnected vertices.
>
>
>
> I try to reconnect the vertices in FreeSurfer but with no success so far..
>
>
>
> Is there a way to overpass this problem in a way I can save my label 
> as a connected surface?
>
>
>
> Thanks in advance
>
> Elisabeth
>
>
>
>
>
>
>
> __________________________________________________________
>
>
>
> Dr Elisabeth Fonteneau
>
> Department of Psychology
>
> University of Cambridge
>
> Downing Street, Cambridge CB2 3EB, UK
>
> Email:  <mailto:ef309 at cam.ac.uk> ef309 at cam.ac.uk
>
> Web:  
> <http://www.neurolex.psychol.cam.ac.uk/directory/ef309@cam.ac.uk>
> www.neurolex.psychol.cam.ac.uk/directory/ef309 at cam.ac.uk
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis


-------------------------
Sheraz Khan, M.Eng, Ph.D.
Instructor in Neurology

Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General
Hospital Harvard Medical School

McGovern Institute for Brain Research
Massachusetts Institute of Technology

Tel:   +1 617-643-5634
Fax:   +1 617-948-5966
Email: sheraz at nmr.mgh.harvard.edu
       sheraz at mit.edu
Web:   http://sheraz.mit.edu
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