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Bug 2091 - simbio seems to be missing for windows

Status NEW
Reported 2013-04-04 11:59:00 +0200
Modified 2016-03-15 11:59:04 +0100
Product: FieldTrip
Component: core
Version: unspecified
Hardware: PC
Operating System: Mac OS
Importance: P3 normal
Assigned to: Simon
Depends on:
See also:

Munsif Jatoi - 2013-04-04 11:59:40 +0200

>> Robert created an account for Munsif and copied this from an email On 4 Apr 2013, at 4:54, Munsif Jatoi wrote: I am doing PhD in EEG Source localization using FEM. I was using the codes available at your website for implementation of head model using FEM. I have written following program in MATLAB: addpath('C:\Users\Munsif\Desktop\Data From Laptop\fieldtrip'); addpath('C:\Users\Munsif\Desktop\Data From Laptop\fieldtrip\utilities'); addpath('C:\Users\Munsif\Desktop\Data From Laptop\fieldtrip\external\freesurfer'); addpath('C:\Users\Munsif\Desktop\Kelantan Dr. Bornot\fieldtrip\external\simbio'); mri = ft_read_mri('G:\tutorial_fieldtrip\Subject01\Subject01.mri'); % reslice cfg = []; cfg.dim = mri.dim; mri = ft_volumereslice(cfg,mri); % segmentation cfg = []; cfg.output = {'gray','white','csf','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % mesh cfg=[]; cfg.method = 'hexahedral'; mesh = ft_prepare_mesh(cfg,segmentedmri); % simbio cfg = []; cfg.method ='simbio'; cfg.conductivity = [0.1 0.2 0.3 0.4 0.5]; % order follows tissuelabel in vol vol = ft_prepare_headmodel(cfg, segmentedmri); when I run this programme by using MATLAB with Fieldtrip, There were some errors stating that a file tp5084846f_e0f2_4004_9e7c_8_6fe72f5707.v which is mesh file is missing. Upon investigation, I come to know that SIMBIO which is used for FEM implementation is missing form Fieldtrip package.

Munsif Jatoi - 2013-04-04 13:33:22 +0200

*** Bug 2092 has been marked as a duplicate of this bug. ***

Johannes Vorwerk - 2013-04-04 15:16:04 +0200

(In reply to comment #0) Hi, unfortunately an external program (vgrid), which is only available for linux and mac os x, has to be used for the mesh creation so far. We are currently working on a matlab-implementation of the mesh generation to circumvent this problem. Hopefully, we will be able to provide a first version in a few weeks. Best, Johannes

Munsif Jatoi - 2013-04-04 18:07:10 +0200

(In reply to comment #2) Ok. Thanks a lot for your reply. It will be really helpful for me to have the MATLAB code as currently I am stuck in this part. Kindly inform me on as soon as you develop the code. Kind Regards, Munsif.

Jan-Mathijs Schoffelen - 2016-02-22 09:36:49 +0100

Since Lilla does not work on FieldTrip anymore, I don't think that it makes sense to keep this assigned to her. Also, assigning it back to the team won't speed up its resolution. Since the bug has 'simbio' in its title I suggest to assign it to Simon, who may be the best one to review it, and either follow up on it, or close it.

Simon - 2016-03-15 11:21:51 +0100

On the skype meeting today Johannes told that all the whole simbio pipeline is coded in matlab. The only exception is the part where the stiffness matrix is computed. This is done through a MEX-file. I check if they are working on different OS.

Simon - 2016-03-15 11:23:48 +0100

(In reply to Simon from comment #5) By checking out external/simbio I realised that also write/read_vista_mesh is a MEX-file

Johannes Vorwerk - 2016-03-15 11:59:04 +0100

(In reply to Simon from comment #6) Yes, that's true I forgot about that. Since it's a routine only for reading vista-meshes to matlab I would assume that it only seldomly needed. To enable previous SimBio-users to switch to FieldTrip-SimBio we should nevertheless try to keep it.