[Mne_analysis] plot_label_from_stc

[Elisabeth Fonteneau]

Thanks you so much Sheraz!
It worked perfectly!
Best,
Elisabeth



-----Original Message-----
From: Sheraz Khan, PhD [mailto:sheraz at nmr.mgh.harvard.edu] 
Sent: 08 February 2017 23:19
To: Elisabeth Fonteneau
Cc: sheraz at nmr.mgh.harvard.edu; 'Discussion and support forum for the users
of MNE Software'
Subject: RE: [Mne_analysis] plot_label_from_stc

please use following commands, they are data independent, requires only
anatomical information. mne.setup_source_space is the one you need for the
src file.


conductivity = (0.3,) #MEG only
model = mne.make_bem_model(subject=subject, ico=4,
                           conductivity=conductivity,
                           subjects_dir=subjects_dir) bem =
mne.make_bem_solution(model) src = mne.setup_source_space(subject,
spacing='ico5',
                             subjects_dir=subjects_dir,
                             add_dist=False, overwrite=True)

Sheraz


> 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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>


-------------------------
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