Errors when the GUI was executed

[sahbi_m]

Hello,

I have installed the ToolBox Lead-DBS from you website and also the SPM12. Then I renamed the files as it was described . But when I executed lead I found many errors like :
Item ‘Tensor Calculation’, field ‘prog’: Value must be a function or function handle on MATLAB path.
Item ‘Probabilistic Tracking’, field ‘prog’: Value must be a function or function handle on MATLAB path.
Item ‘Mori Streamline Tracking’, field ‘prog’: Value must be a function or function handle on MATLAB path.
Item matlabbatch: No repeat named
spm
Undefined function ‘list’ for input arguments of type ‘cell’.

Error in cfg_repeat/list (line 112)
[id1, stop1] = list(citems{k}, spec, tropts);

Error in cfg_util>local_getcjid2subs (line 1352)
cjid2subsin = list(cjin, exspec, tropts);

Error in cfg_util>local_initjob (line 1537)
[ucj, ucjid2subs] = cellfun(@local_getcjid2subs, ucj, ‘UniformOutput’, false);

Error in cfg_util (line 802)
[jobs(cjob), mod_job_idlist] = local_initjob(jobs(cjob), job, jobdedup);

Error in cfg_util (line 953)
cjob = cfg_util(‘initjob’,varargin{1});

Error in ea_create_mni_darteltemplate (line 36)
cfg_util(‘run’,jobs);

Error in ea_normalize_spmdartel (line 105)
ea_create_mni_darteltemplate([options.root,filesep,options.patientname,filesep,’rc1′,options.prefs.prenii_unnormalized]);

Error in ea_autocoord (line 84)
eval([options.normalize.method,'(options)’]); % triggers the normalization function and passes the options struct
to it.

Error in lead>run_button_Callback (line 337)
ea_autocoord(options);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in lead (line 42)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

Kind regards,
Sahbi mallouli

[andreashorn]

Dear Sahbi,

this is weird. Did you try to open SPM 12 itself alone? (i.e. type spm fmri) and see if that starts up?

Best, Andy

[sahbi_m]

Dear Andy,

I tried with spm fmri alone and it worked ( with the four files :anat.nii,postop_tra.nii ,postop_cor.nii ,postop_sag.nii)

But when I ran lead DBS with the following optins ( [x]Normalize+ [x] check Normalisation+[x]reconstruct(with STN, GPI or Vim option for Entry point target and auto mask)+ [x] Review reconstruction+ visualisation) it wrote many results in the workspace matlab but in the end it got stuck with the errors listed above. Please find here the list of files I got after running lead DBS ( c1,c2,c3-anat.nii+iy_anat.nii+raw_postop_cor,sag,tra.nii+rc1,2,3-anat.nii+ y_anat.nii+ anat_seg8.m+ea_ui.m+ ea_normmethod_aplied.m+ the four old files , So 15 new files in the end)

Thanks,
Sahbi

[andreashorn]

Okay. I need to fix this at some point.
In the meantime, please download and unzip this file (https://dl.dropboxusercontent.com/u/18255196/dartelmni_6_hires.nii.zip) and put it into your lead/templates/dartel/ folder. Re-run again. I’d also advise that you run each step separately to be able to debug a bit better if you’re still unfamiliar with the toolbox.

Best, Andy

[sahbi_m]

Hi Andy,

Now it works and shows me two wireframes for pre and postoperative but it ends up with an Error Dialog (in Gui frame) : “please put a suitble anatomy file inside patient folder” however it already worked with SPM12 and actually for the same files.

Thanks,Sahbi

[andreashorn]

Mh, are you sure you are indeed using SPM12 (and not a different version)? Please make sure that SPM8 is not on your path and if you start spm, version 12 it starts up. This particular check-function (ea_checkfiles) is only working with SPM12 and will show an error if using SPM8 (not supported anymore).

You could temporarily comment line 34 of ea_checkfiles.m and everything should still work.

Best, Andy

[sahbi_m]

Thank you for you previous email, actually I did what you said but always at the end it shows me a small frame in GUI window which contains the same old message : “please put a suitble anatomy file inside patient folder”
And in the workspace of matlab (R2016a): it wrote me the following errors:
Error using ea_error (line 8)
Please put a suitable anatomy file inside patient folder

Error in ea_checkfiles (line 34)
ea_error(‘Please put a suitable anatomy file inside patient folder’);

Error in ea_autocoord (line 123)
ea_checkfiles(options);

Error in lead>run_button_Callback (line 337)
ea_autocoord(options);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in lead (line 42)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

Kind regards
sahbi

[sahbi_m]

Dear Andy,

This time I executed lead DBS with only checking (Normalize + check Normalization) it worked for coronar and axial (by showing me two matlab figures of coronar and transversal) but not for sagital!! So there is always problem in the corgestration step.

It always shows me these types of errors:

Undefined function or variable ‘coords_mm’.

Error in ea_load_reconstruction (line 47)
markers(side).head=coords_mm{side}(1,:);

Error in ea_writeplanes (line 27)
coords_mm=ea_load_reconstruction(options);

Error in ea_write (line 26)
cuts=ea_writeplanes(options);

Error in ea_autocoord (line 222)
ea_write(options)

Error in lead>run_button_Callback (line 337)
ea_autocoord(options);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in lead (line 42)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

Index exceeds matrix dimensions.

Error in ea_imshowpair/mouseClick (line 270)
i2=i2(2);

Error while evaluating Figure ButtonDownFcn

Best, sahbi

[sahbi_m]

Dear Andy,

I tried many times but always the same errors appear in the reconstruction step :
Error using spm_vol>spm_vol_hdr (line 80)
File “C:\Users\Sahbi\Desktop\p1034\patient1034\y_ea_normparams.nii” does not exist.

I realized that the problem is always in the reconstruction step.
So could you please help me how can I find this missing file : y_ea_normparams.nii.

Best
Sahbi

[andreashorn]

Dear Sahbi,

sorry you are having so much trouble getting it to work.
Usually, the y_ea_normparams.nii file will be generated if you run an SPM-based normalization within Lead-DBS (DARTEL, Segment). However, I’d recommend to use Advanced Normalization Tools for now – it’s just much better tested because we use it ourselves. I’d still like to find out how the problem originated. Could you please do the following:

1. Run (only) Normalization again (DARTEL) and check if ea_normparams.nii really isn’t being generated and if so, if an error message appeared. Please always post full error messages (the whole red text in Matlab), otherwise, they are often useless for me.

2. If the file really doesn’t appear, try running the ANTs based normalization and see if things work from here.

If both doesn’t work, we should get in contact via mail and you’d need to somehow send me the dataset in an anonymized way so I could debug and see where the problem originated.

Best, Andy

[sahbi_m]

Hi Andy,

Thank you very much for your last email. Actually, it worked with Dartel but it didn’t show right results, and the issue was that the 2 leads in the final 3D image weren’t in the right place.

Please find here my email: malloulisahbi@gmail.com So I can send my anonymized files.

Best, sahbi

[sahbi_m]

Hi,

please find here the errors after the reconstruction step (and the normalization was done with ANTs):

Error using spm_vol>spm_vol_hdr (line 80)
File “C:\Users\Sahbi\Desktop\Tuesday_results\patient_tues\y_ea_normparams.nii” does not exist.

Error in spm_vol (line 61)
v = spm_vol_hdr(deblank(P(i,:)));

Error in ea_checkforwardinv (line 5)
V=spm_vol([options.root,options.patientname,filesep,’y_ea_normparams.nii’]);

Error in ea_reconstruction2native (line 16)
ea_checkforwardinv(options,’forward’)

Error in ea_load_reconstruction (line 20)
ea_reconstruction2native(options);

Error in ea_manualreconstruction (line 38)
[coords_mm,trajectory,markers,elmodel,manually_corrected]=ea_load_reconstruction(options);

Error in ea_autocoord (line 219)
ea_manualreconstruction(mcfig,patientname,options);

Error in lead>run_button_Callback (line 337)
ea_autocoord(options);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in lead (line 42)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

Have a nice day,
sahbi

[sahbi_m]

Hi Andy,

I am so sorry for all these messages. I actually realized that after a stimulation (in the final 3D framework) there is always an error message. If you could kindly take a look at it just below.

Best,
sahbi
Error using mkdir
The filename, directory name, or volume label syntax is incorrect.

Error in ea_genvat_maedler (line 109)
mkdir([options.root,options.patientname,filesep,’stimulations’,filesep,stimname]);

Error in ea_stimparams>stimulate_Callback (line 948)
[stimparams(1,side).VAT(el).VAT,volume]=feval(ea_genvat,elstruct(el).coords_mm,S,side,options,stimname);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in ea_stimparams (line 42)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)ea_stimparams(‘stimulate_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

[rubenscury]

Hi Sahbi,

How have you fix this issue?
I’m having the same problem right now. I cannot reconstruct the VTA….

Error in ea_genvat_horn (line 117)
tess = mesh.tet(:,1:4);

Error in ea_stimparams>stimulate_Callback (line 950)
[stimparams(1,side).VAT(el).VAT,volume]=feval(ea_genvat,elstruct(el).coords_mm,getappdata(handles.stimfig,’S’),side,options,stimname,options.prefs.machine.vatsettings.horn_ethresh,handles.stimfig);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in ea_stimparams (line 42)
gui_mainfcn(gui_State, varargin{:});

Error in
@(hObject,eventdata)ea_stimparams(‘stimulate_Callback’,hObject,eventdata,guidata(hObject))

Error while evaluating UIControl Callback

Thanks
Best
Rubens Cury

[andreashorn]

Hi Rubens,

could you please send the full error message? The first (most crucial) line is missing..

If you haven’t done so, it might also make sense to watch the walkthrough video to check if things look the same on your side:

Walkthrough-Videos

Best, Andy

[Author]

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