[FieldTrip] Headmodel with NeuroScan meshes

Tue Jun 12 10:08:32 CEST 2012

Deal Alex,

Thank you so much for the quick reply, I managed to do what you suggested then got stuck at loading the '_sm_flip.tri' files to MATLAB.

This may be a very naive question, but hope you can give me some help on this please.

Many thanks

Kind regards


From: alexandre.gramfort at gmail.com [alexandre.gramfort at gmail.com] on behalf of Alexandre Gramfort [alexandre.gramfort at inria.fr]
Sent: Tuesday, 12 June 2012 4:10 PM
To: FieldTrip discussion list; IMALI THANUJA HETTIARACHCHI
Subject: Re: [FieldTrip] Headmodel with NeuroScan meshes

hi Imali,

your meshes had indeed tiny problems. To fixed it I just smoothed a tiny bit the meshes.

In matlab:

>> load innerSkull
>> om_save_tri('innerSkull.tri', curryloc', currytri');

then :

$om_mesh_smooth -i innerSkull.tri -o innerSkull_sm.tri -n 2
$om_mesh_convert -i innerSkull_sm.tri -o innerSkull_sm_flip.tri -invert
$ om_mesh_info -i innerSkull_sm_flip.tri
om_mesh_info version 2.2.dev (exported) compiled at Mar  7 2012 15:37:20

load_tri : innerSkull_sm_flip.tri
Mesh Info :
# points : 2934
# triangles : 5864
Euler characteristic : 2
Min Area : 6.55783
Max Area : 28.9211
Mesh orientation correct (valid for closed mesh).

this should fix the problem. Note that you can surely also smooth the meshes in matlab.

Alexandre Gramfort, PhD
alexandre.gramfort at inria.fr<mailto:alexandre.gramfort at inria.fr><mailto:alexandre.gramfort at inria.fr>
INRIA Parietal Project Team, NeuroSpin CEA Saclay
Bat. 145, PC 156
91191 Gif-sur-Yvette, France

On Tue, Jun 12, 2012 at 3:25 AM, IMALI THANUJA HETTIARACHCHI <ith at deakin.edu.au<mailto:ith at deakin.edu.au>> wrote:

Dear FieldTrip users,

As I have faced problems in creating a head model with MRI's, so I thought to try the MNI head for creating the meshes. I used the NeuroScan software to create the surface meshes and exported them to Matlab. Then tried to crate the head model using ft_prepare_headmodel function.  however the 'om_minverser' stops working and the program terminates.

When I plot the meshes they seem fine to me so I assume that there is no segmenting issues. But Now I get an error as attached in the 'log.txt' from the Matlab workspace, which says about self intersecting meshes. I have attached the Neuroscan exported meshes (innerSkull.mat,outerSkull.mat,skin.mat) and the Matlab function (m_file.txt) that I used in creating the head model.

I really want to generate some simulated EEG data but cannot make anything work. If someone can give a guidance on where I am going wrong in the procedure , that will be highly appreciated.

Many thanks.

Kind regards


Imali Thanuja Hettiarachchi
PhD Candidate
Centre for Intelligent Systems research
Deakin University, Geelong 3217, Australia.

Mobile : +61430321972<tel:%2B61430321972>
Email: ith at deakin.edu.au<mailto:ith at deakin.edu.au>

[Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD at deakin.edu.au]

fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>

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.

Alexandre Gramfort, PhD
alexandre.gramfort at inria.fr<mailto:alexandre.gramfort at inria.fr>
INRIA Parietal Project Team @ NeuroSpin CEA Saclay
Bat. 145, PC 156
91191 Gif-sur-Yvette, France
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120612/46350390/attachment-0002.html>

More information about the fieldtrip mailing list