[rubenscury]

Ok, many thanks for the prompt reply
Best
Rubens

[rubenscury]

Thanks Andy,

The “brain parcellation” problem I solved, it is working normally…

The “t-test” issue I’ll try later and see….

Best
Rubens

[rubenscury]

Very nice Andy, thanks a lot

I am also trying to change the “brain parcellation” in the Lead Group. For exemple, move from AICHA to Harvard Oxoford…..
In the Lead Group, all the patients and the variables are already set. But when I change in the link “which brain parcellation to use:” from AICHA to Harvard Oxoford and run “Prepare Stats”, in the “fiber count to” still appears the AICHA parcellation (G_Frontal_Sup_Orb…etc…)…i.e. it is not changing the brain area….

Would you have any insight for what is going wrong?

Again, thanks for your attention
Best
Rubens

[rubenscury]

Thanks Andy,

I am comparing group 1 (N=20) vs group 2 (N=10)….it still appears the following message in the matlab workspace:
Volume Intersections, both hemispheres

h =

NaN

p =

NaN

ci =

NaN
NaN

and so on….

The correlation is working very well, but the group comparison I am not sure what is happening…

Many thanks
Rubens

[rubenscury]

Dear colleagues,

In order to walk through all lead-dbs tools, what package in Matlab should I download? 1) computational finance, 2) control system, 3) image processing and computer vision, 4) signal processing, 5) computational biology and 6) data analytics?

I did not find this information in the manual,

Regards
Rubens

[rubenscury]

Thanks Andy,
I was using Matlab 2014b. Now I installed the 2018a version and the “corr” function is working normally.

Many thanks again
Best, Rubens

[rubenscury]

Actually now it works. I was setting the SimBio model for VTA, but trying the other ones the “prepare stats” runs perfectly. The problem now is in the next step: correlate variable (updrs improvement) with VTA intersection

The following error appears:

VI_BH
Undefined function ‘corr’ for input arguments of type ‘double’.

Error in ea_permcorr (line 17)
r(a) =corr(x(:,a),y,’type’,type,’rows’,’pairwise’);

Error in ea_corrplot_gen (line 39)
[R,p]=ea_permcorr(X(:,1),X(:,2),’spearman’);

Error in lead_group>corrbutton_vta_Callback (line 571)
[R_upd,p_upd,R,p,f]=ea_corrplot_gen([stats.corrcl,stats.vicorr.nboth],description,stats.vc_labels,[],[],’permutation’);

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

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

Error in
@(hObject,eventdata)lead_group(‘corrbutton_vta_Callback’,hObject,eventdata,guidata(hObject))

Error while evaluating UIControl Callback

Does anybody can help me?
Many Thanks
Rubens

[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

[rubenscury]

Nice Andy,
I’ll try to use this nice tool,
Tks
Best,
Rubens

[rubenscury]

Dear colleagues,

We’ve been working with DBS targeting the cerebellum (dentate nucleus). Does anyone know if there is any atlas in the Lead-DBS that see the cerebellum? If the answer is not, can I import an atlas into the Lead-DBS?

Best
Rubens

[rubenscury]

Dear Andreas,
I’m trying to coregister the images but it is not working…the error below appears in the matlab,
I’m using anat_1.ii anat_2.nii postop_ct.nii…..

I’ve already deleted and reinstalled the lead DBS, but the error continues….
Can you help me?
Many thanks

ANTs LINEAR registration done.
Coregistration done.
Tonemapping CT… Done. (2.1754 s)

Exporting coregistration check images to /Users/rubenscury/Desktop/vanilson sn/checkreg…
Tonemapping CT… Done. (0.8466 s)
Images aren’t the same size!
Done.
Undefined function or variable ‘cfg_util_persistent’.

Error in cfg_util (line 433)
[c0, jobs] = cfg_util_persistent;

Error in spm_jobman (line 246)
cjob = cfg_util(‘initjob’, mljob);

Error in ea_docoreg_spm (line 49)
spm_jobman(‘run’,{matlabbatch});

Error in ea_coreg2images (line 37)
affinefile =
ea_docoreg_spm(options,appendcommaone(moving),appendcommaone(fixed),’nmi’,1,commaoneotherfiles,writeoutmat,interp);

Error in ea_coreg_all_mri (line 16)
ea_coreg2images(options,[directory,presentfiles{coregfi}],[directory,presentfiles{1}],[directory,presentfiles{coregfi}]);

Error in ea_checkcoregallmri (line 9)
ea_coreg_all_mri(options,usebrainmask)

Error in ea_autocoord (line 140)
ea_checkcoregallmri(options,0,1); % check and coregister all
preoperative MRIs here.

Error in ea_run (line 96)
ea_autocoord(options);

Error in lead_dbs>run_button_Callback (line 187)
ea_run(‘run’,options);

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

Error in lead_dbs (line 43)
gui_mainfcn(gui_State, varargin{:});

Error in
@(hObject,eventdata)lead_dbs(‘run_button_Callback’,hObject,eventdata,guidata(hObject))

Error while evaluating UIControl Callback

[Author]

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