[tsieger]

Is the E-field “tube” expected to follow the electrode artifact?
Also, I realized there is the “Auto-segment electrode from postoperative acquisition” button in the 3D view, but it seems it does nothing for my data (postop CT).

Cheers,
Tomas

[tsieger]

even though it seems that the electrode is not that much bent:
http://neuro.felk.cvut.cz/data/uploads/images/misc/leaddbs-left-electrode.png
–tbc–

[tsieger]

I can’t even start a new topic. I’ll try to continue here:

I’m curious why the E-field deviates quite a lot from my electrode:
http://neuro.felk.cvut.cz/data/uploads/images/misc/leaddbs-vat.png

–tbc–

[tsieger]

I’m encountering problems posting replies to this thread. I’ll try to start another topic.
Tomas

[tsieger]

Hi Ningfei,
thanks for your quick help.
Yes, the hotfix resolved the issue (when downloaded and applied manually). VTA then could be computed w/o problems.
BTW: installing the hotfix from the Install menu did not work: http://neuro.felk.cvut.cz/data/uploads/images/misc/leaddbs2.3-update.png

• This reply was modified 4 years, 9 months ago by tsieger.

[tsieger]

However, now I run into a problem with:

Subscripted assignment dimension mismatch.
Error in ea_genvat_horn>jr_remove_electrode (line 712)
r_pos(:,r_pos(2,:)>0) = cr_pos;
Error in ea_genvat_horn (line 355)
vat = jr_remove_electrode(vat,elstruct,mesh,side,elspec);
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 matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)ea_stimparams('stimulate_Callback',hObject,eventdata,guidata(hObject)) 
Error while evaluating UIControl Callback

size of rpos:
3 98658

size of r_pos(:,r_pos(2,:)>0):
3 89817

size of crpos:
3 179622

[tsieger]

Another problem in vecnorm, which was introduced in R2017b.
https://github.com/netstim/leaddbs/pull/322

Please note that this PR also fixed the problem with incompatible matrix sizes:

Error using -
Matrix dimensions must agree.
Error in ea_genvat_horn>jr_remove_electrode (line 678)
tra = elstruct.trajectory{1,side} - org;
Error in ea_genvat_horn (line 355)
vat = jr_remove_electrode(vat,elstruct,mesh,side,elspec);
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 matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)ea_stimparams('stimulate_Callback',hObject,eventdata,guidata(hObject)) 
Error while evaluating UIControl Callback

(I’ve used an explicit repmat to fix this.)

[tsieger]

Another problem in interactive 3d viewer control:

Error in ea_mouse_camera/motion_callback (line 63)
        pt = matlab.graphics.interaction.internal.getPointInPixels(hfig,currpt(1:2)); 
Error while evaluating Figure WindowButtonMotionFcn

this unfortunatelly also does not work on R2016a :-(.

[tsieger]

Hi, I ran into another Matlab dependency problem with the newline function and create a PR fix for it: https://github.com/netstim/leaddbs/pull/321.

[tsieger]

Hi Ningfei,
I tracked the issue down. This is also a Matlab dependency problem. The problem is in ea_delete.m, which makes use of the .folder field in the return value from the dir function.
In the current Matlab 2019b, the entries returned contain the following fields:

   name
    folder
    date
    bytes
    isdir
    datenum

but in R2016a, they contain only:

    name
    date
    bytes
    isdir
    datenum

This problem demonstrates in ea_create_tpm_darteltemplate, where a loop is made (l.147-194), cleaning using ea_delete on each iteration, and crashing at the end of the first iteration, never reaching the others, such that not all templates get created.

[tsieger]

Great, thanks a lot.
Tomas

[tsieger]

OK, VTA can be computed in native space.
However, it seems that electrode reconstruction can be performed in normalized space only, as when I attempt to pre-reconstruct electrodes without normalizing first, it fails with: glpostop_tra.nii" does not exist., even though I choose the ‘Native Patient Space’ option under ‘7. Visualization’.
Maybe, I’m missing something.

[tsieger]

Re contains: I’ve issued this PR: https://github.com/netstim/leaddbs/pull/320

Re Shoot: I had no specific reason to use it, but it seems that ‘SPM12 Shoot’ is the default normalization option.

[tsieger]

Thanks. Still, is it possible to extract electrodes in native space, in patient’s MRI being not affected in a nonlinear way?

[tsieger]

Regarding the contains() issue: I’m afraid my hack was too hacky and could not be used as a proper replacement for the original function, as it e.g. does not support patterns consisting of several strings, which the original function does support. Also, contains() can be used in both case-sensitive and insensitive modes, while strfind cannot. However, looking in the Lead-DBS code, multiple-string patterns seem not to be used, and possibly neither case-insensitive search.
So, I suppose there are three possible solutions:
i) put the hacked version of contains() in the code *only* for Matlab <R12016b (I can’t see a way how to do this when there is no installation process and users can get the code directly from github),
ii) put the hacked version of contains() in the code regardless of Matlab version (this would IMHO produce tons of warnings, I would not go this way),
iii) put a differently named function (e.g. mycontains() in the code and update all the calls to contains() to mycontains() – this would affect quite many people and much code, but would be quite clean IMHO.
What’s your opinion?

Regarding the normalization issue: ignoring the keyboard did not help, the process failed with

------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Run Shoot (existing Templates)'
Failed  'Run Shoot (existing Templates)'
Error using read_hdr (line 32)
Error reading header file "/home/sieger/src/matlab/leaddbs-2.2.3/templates/space/MNI_ICBM_2009b_NLIN_ASYM/dartel/shootmni_1.nii".
In file "/home/sieger/src/matlab/spm12/@nifti/private/read_hdr.m" (v4967), function "read_hdr" at line 32.
In file "/home/sieger/src/matlab/spm12/@nifti/nifti.m" (v4986), function "nifti" at line 26.
In file "/mnt/hdd/home/sieger/src/matlab/spm12/toolbox/Shoot/spm_shoot_warp.m" (v6024), function "load_template" at line 195.
In file "/mnt/hdd/home/sieger/src/matlab/spm12/toolbox/Shoot/spm_shoot_warp.m" (v6024), function "spm_shoot_warp" at line 104.

The following modules did not run:
Failed: Run Shoot (existing Templates)

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message)
------------------
Running job #1
------------------

The problem was that the .../MNI_ICBM_2009b_NLIN_ASYM/dartel/shootmni_1.nii is missing.
There are only these files in the directory:

dartelmni_6.mat
dartelmni_6.nii
dartelmni_6_hires_00001.nii
dartelmni_6_hires_00002.nii
dartelmni_6_hires_00003.nii
dartelmni_6_hires_00004.nii
dartelmni_6_hires_00005.nii
dartelmni_6_hires_00006.nii
s0dartelmni_6_hires_00001.nii
s0dartelmni_6_hires_00002.nii
s0dartelmni_6_hires_00003.nii

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