[FieldTrip] quick fix? ft_sourceplot error line 460
Hassan Aleem
ha438 at georgetown.edu
Fri Mar 11 07:46:18 CET 2016
Thanks for your response J.M. That makes sense. I will remove all
eeglab/spm/fieldtrip and reinstall,making sure to keep fieldtrip separate.
On Mar 11, 2016 1:40 AM, "Schoffelen, J.M. (Jan Mathijs)" <
jan.schoffelen at donders.ru.nl> wrote:
> 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 incorrect/outdated copy of issubfield.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> 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> 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> 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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>> fieldtrip at donders.ru.nl
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>>
>>
>>
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>
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