Reconstructing leads of unusual targets

[cloz]

Hi there,
I am trying to use lead DBS to reconstruct leads of the fornix, PAG, thalamus, etc.
In the reconstruction step, I choose manual reconstruction but either the electrode tract is not visible in the window or the red box doesn’t overlap with the tract. Is there any way to adjust the view of the scan at this step so that we can select the electrode tract properly?

Thanks

[andreashorn]

Hi cloz,

the red area doesnt need to overlap with the artifact, it just shows you the side you need to click on.

Should work ez&well with Fornix electrodes.

Best, Andy

[cloz]

Hi Andy,
Thanks for your reply. Good to know that about the red box. We are still having problems though. When we try to select the artifact for our scan, we get the following error in Matlab:
Index exceeds matrix dimensions.

Error in ea_sample_cuboid (line 92)
if trajvector(3)<0

Error in ea_reconstruct_coords (line 3)
[cimat,reldist]=ea_sample_cuboid(trajectory,options);

Error in ea_reconstruct (line 123)
[coords,goodz]=ea_reconstruct_coords(trajectory,trajvector,options);

Error in ea_autocoord (line 138)
                    [coords,trajvector{side},trajectory{side},tramat]=ea_reconstruct(options.patientname,options,options.sides(side));
                    
Error in ea_run (line 95)
                    ea_autocoord(options);

Error in lead_dbs>run_button_Callback (line 201)
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
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_dbs('run_button_Callback',hObject,eventdata,guidata(hObject)) 
Error while evaluating UIControl Callback

We find that at the slice that is shown in the window it is very hard to see where exactly where the artifact is since the view we have shows it very close to the ventricle. Is there any way we can adjust the slice we are viewing during the reconstruction step?

Thanks again for your help!

[andreashorn]

Hi cloz,

you can change the height in the ea_spacedef.mat file in /templates/space/MNI_ICBM_2009b_NLIN_ASYM
or in the code at ea_reconstruct_trajectory > ea_getstartslice on line 312.

A postop T2 is definitely easier to reconstruct the lead if the lead crosses the ventricles (since in T1 both are dark).

Hope this helps!

Best, Andy

[cloz]

Hi Andy,
That’s perfect, thank you very much!

[Vlevi]

Hi Andy,
I’ve recently been trying to reconstruct a pair of electrodes implanted in the anterior cingulate cortex ( ACC) , but I’ve got same Cloz’s error. I haven’t understood how to change the height in the ea_spacedef.mat file and adjust the slice during the reconstruction step.

thanks for your help,

Vincenzo

[andreashorn]

Hi Vlevi,

we recently added a purely manual approach to localize electrodes in unusual targets that is currently only available in the github version (but will be released on the website at some point, too).
So if you’re in a rush, you can head to the lead-dbs manual and see “install via github” section – or wait for the next release.

Best, Andy

[Vlevi]

Hi Andy,
that’s great, I’ll be waiting the next release. Thank you!

[yez]

Hi Andy,
I’m new to Lead-DBS. I’m wondering whether the pre-reconstruction-related functions have been updated and released.

I ran lead-DBS on win8 + matlab2015b, and got a similar problem as those of cloz and Vlevi. If I understand correctly, the pink box appears when one sets entry point to ‘STN/GPi/VIM’; and windows for selecting the starting point of the artifact should appear when one sets entry point to ‘manual’. But after choosing ‘manual’, I got the pink box, not the corrct windows.
Do you have any idea why and how to fix the problem?

Thanks in advance!

[Author]

Posts