[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

[sahbi_m]

I’m sorry for this message it wasn’t in the right place.
it will be posted in the other conversation.

best regards,
sahbi

[sahbi_m]

Hi Andy,

Thank you for your reactivity. Actually there was a pretty good progress in my work but unfortunatly usually after the manual correction it shows me up an error message. If you could kindly find below this message which was generated after each saving results (with the espace bar) of a manuel correction.

All my best
sahbi

Reference to non-existent field ‘rawpreniis’.

Error in ea_assignpretra (line 6)
for prenii=1:length(options.prefs.rawpreniis)

Error in ea_native2acpc (line 47)
options=ea_assignpretra(options);

Error in ea_reconstruction2acpc (line 12)
fid=ea_native2acpc(cfg,{directory});

Error in ea_save_reconstruction (line 24)
ea_reconstruction2acpc(options);

Error in ea_manualreconstruction>ea_endfcn (line 120)
ea_save_reconstruction(coords_mm,trajectory,markers,elmodel,1,options);

Error in ea_manualreconstruction>ea_keystr (line 167)
ea_endfcn(mcfig);

Error while evaluating Figure KeyPressFcn

[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,

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]

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

[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]

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]

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

[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

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