[FieldTrip] quick fix? ft_sourceplot error line 460
Schoffelen, J.M. (Jan Mathijs)
jan.schoffelen at donders.ru.nl
Fri Mar 11 07:36:17 CET 2016
I cannot reproduce your problem. It seems that you are using an incorrect/outdated copy of issubfield. The line number you report in your error message does not line up with the current version. Please ensure that your matlab path is set correctly, in particular try to avoid copies of SPM or eeglab taking precedence. These may have old versions of FT code that can cause all kinds of erratic behaviour.
Best wishes,
Jan-Mathijs
On 11 Mar 2016, at 01:02, Hassan Aleem <ha438 at georgetown.edu<mailto:ha438 at georgetown.edu>> wrote:
Hi J.M,
I am using fieldtrip2016-03-09 and Matlab R2015b with a debian linux operating system. However the problem appears also on my windows 10 OS. I am unable to take a look at the 'seg' or 'mri' because the ft_sourceplot does not work with the same complaint as with trying to plot the source interpolation, I assume that's what you mean by checking them. Let me post the script to give you more information. ( the headmodel part of the script was modified from robert bauer)
%reading mri
[mri] = ft_read_mri('MNI152_T1_0.5mm.nii');
mri.coordsys ='MNI'
-----------------------------------
%segmentation
cfg = [];
cfg.brainthreshold = 0.5;
cfg.scalpthreshold = 0.15;
cfg.downsample = 1; %no downsampling
cfg.output = {'brain' 'scalp' 'skull'};
seg = ft_volumesegment(cfg, mri);
----------------------------------
%plotting segmentation
cfg = [];
cfg.funparameter = 'trishells';
cfg.funcolormap = [1 0 0;0 1 0;0 0 1];
ft_sourceplot(cfg,seg) this does not work, same error.
------------------------------------------
%building mesh
cfg = [];
cfg.method= 'projectmesh';
cfg.tissue = {'scalp', 'skull', 'brain'};
cfg.numvertices = [1000 1000 1000];
bnd = ft_prepare_mesh(cfg, seg);
% i enlarged / reduced the boundary mesh a little bit, because they were causing errors, probably due to overlapping
bnd(1).pnt = bnd(1).pnt.*1.001
bnd(2).pnt = bnd(2).pnt.*1
bnd(3).pnt = bnd(3).pnt.*0.999
ft_plot_mesh(bnd(1))%scalp
ft_plot_mesh(bnd(2))%skull
ft_plot_mesh(bnd(3))%brain
----------------------------------------------------------
%preparing headmodel
cfg = [];
cfg.method = 'dipoli';
headmodel = ft_prepare_headmodel(cfg, bnd);
--------------------------------------------------------
%adding electrodes to headmodel
elec=ft_read_sens('Hydrocel_GSN_128_1.0_TRIM_mod.sfp'); %load electrode file
% visualize head surface (scalp)
figure;
ft_plot_mesh(headmodel.bnd(1), 'edgecolor','none','facealpha',0.8,'facecolor',[0.6 0.6 0.8]);
hold on;
% plot electrodes
ft_plot_sens(elec,'style', 'sk')
% aligning electrodes
cfg = [];
cfg.method = 'interactive';
cfg.elec = elec;
cfg.headshape = headmodel.bnd(1);%scalp
st_elec_aligned = ft_electroderealign(cfg);
-----------------------------------------------
%using the standard template sourcemodel from fieldtrip.
load('standard_sourcemodel3d5mm.mat')
-------------------------------------
%% timelock data
cfg = [];
m0 = ft_timelockanalysis(cfg, dataM0);
--------------------------------------
%% perform source analysis
cfg = [];
cfg.method = 'lcmv';
cfg.lcmv.lambda='5%';
cfg.grid = sourcemodel.cfg.grid;---this is the standard template from fieldtrip
cfg.headmodel = headmodel;
cfg.lcmv.keepfilter = 'yes';
cfg.lcmv.projectnoise='yes';
cfg.lcmv.fixedori = 'yes'; % project on axis of most variance using SVD
source_m0=ft_sourceanalysis(cfg,m0);
------------------------------
%% source interpolation
cfg = [];
cfg.interpmethod = 'nearest';
cfg.parameter = 'pow';
cfg.grid=sourcemodel.cfg.grid;
sourceinterp_m0 = ft_sourceinterpolate( cfg, source_m0, seg);
----------------------------------------------
%plotting
cfg = [];
cfg.method = 'ortho';
cfg.funcolorlim = 'maxabs';
cfg.funparameter= 'pow';
ft_sourceplot(cfg, sourceinterp_m0);
This is where it gives me the error. Please let me know if you need more information. I also had a question about making a 'source' it seems that the fieldtrip tutorial does not use a 'sourcemodel' but instead use a dipolefitting source, is this comparable. Thank you for the help in advance.
Best,
Hassan
On Thu, Mar 10, 2016 at 3:00 AM, Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>> wrote:
Hassan,
Can you please provide a bit more information with respect to what version of fieldtrip, matlab and operating system you use?
Did you check whether the ‘seg’ looks healthy? Does the ‘mri’ plot well? We need more information to work with.
Best,
Jan-Mathijs
On 09 Mar 2016, at 21:26, Hassan Aleem <ha438 at georgetown.edu<mailto:ha438 at georgetown.edu>> wrote:
Hi everyone,
I have a question that is possibly very easy to solve but is evading me. I am unable to get ft_sourceplot to work. For example when I run the code:
[mri] = ft_read_mri('MNI152_T1_0.5mm.nii');
mri.coordsys ='MNI'
cfg = [];
cfg.output = {'brain' 'scalp' 'skull'};
seg = ft_volumesegment(cfg, mri);
seg.anatomy = mri.anatomy;
cfg = [];
cfg.funparameter = 'brain';
ft_sourceplot(cfg,seg)
I get the error:
Error using textscan
First input can not be empty. Expected a non-empty string or a valid file-id.
Error in issubfield (line 44)
t = textscan(f,'%s','delimiter','.');
Error in ft_sourceplot (line 460)
hasmsk = issubfield(functional, cfg.maskparameter);
This is happening regardless of what stage I use ft_sourceplot.
Thanks for your consideration!
Hassan
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