[FieldTrip] quick fix? ft_sourceplot error line 460
Hassan Aleem
ha438 at georgetown.edu
Sun Mar 13 20:42:06 CET 2016
Just to put this out there for reference. I was able to solve the problem
by replacing the 'issubfield' function with its Matlab equivalent 'isfield'.
On Fri, Mar 11, 2016 at 1:46 AM, Hassan Aleem <ha438 at georgetown.edu> wrote:
> 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 incorrect/outdated copy of issubfield.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
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
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>>
>>
>>
>>
>>
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>
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