Technical Questions

[andreashorn]

Please post questions regarding installation / file-handling and bugs here!

[Johannes Keyser]

Hi there!
My main GUI window is rather small and looks jumbled around – can I do somthing about it?
It’s not a deal breaker, but it would be nice if I could read the options in the drop-down menus etc :-).

In MATLAB, ver() yields

MATLAB Version: 8.1.0.604 (R2013a)
MATLAB License Number: XXXXXXXX
Operating System: Linux 3.15.1-1-ARCH #1 SMP PREEMPT Tue Jun 17 09:32:20 CEST 2014 x86_64
Java Version: Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode

• This reply was modified 7 years, 3 months ago by Johannes Keyser.
• This reply was modified 7 years, 3 months ago by Johannes Keyser.
• This reply was modified 7 years, 3 months ago by Johannes Keyser.

[andreashorn]

Dear Johannes,

thanks for this feedback and for trying out the toolbox! We already realized this on a windows machine and adapted the GUI, which has been made on a mac, a bit. However I took the opportunity to re-model the whole GUI to have more space and to get a clearer overview of the workspace this morning. I also entered some tooltip-strings, so if you hover over the GUI elements now, there should be some help displayed. I’ll send you a download-link for the new version soon. Please tell us if the GUI still feels crumpy, because this is very important for the overall user experience, of course.

Cheers, Andy

[Johannes Keyser]

Dear Andreas,

that was quick, thank you very much!
It looks much better now, and I can read everything. The hints/tooltips are also very useful to have!
Now let’s see whether I can get it to run with our data :-).

[JoseP]

Hi Andreas,

it seems leaddbs is not dealing well with my MRI files in the localization of the electrodes.
Both of them were acquired in sagital planes, but after your suggestion I named them after the expected notation tra.nii and pre_tra.nii. However, once I have to check the normalization it does not seems correct to me. Do i need to change manually the orientation in these files to be in the axial planes?

Also, I wanted to visualize the electrodes over the accumbens and caudate nucleus, since accumbens is not in the atlas provided, I thought that Harvard Oxford could be a good choice.
Is it enough with defining rh and lh folders, and the .nii files for each of these structures?

cheers
Jose

[andreashorn]

Hi Jose,

The normalization routines of DBS use (sometimes slightly modified) SPM methods and you could also choose to start off with normalized images directly (normalize them to MNI space using SPM, FSL, Slicer, whatever works). You just have to rename the normalized files to “ltra.nii” and “lpre_tra” respectively.

You can use the accumbems from the HO atlas, simply isolate it from the atlas file for right and left hemisphere (e.g. Using image calculator) and put the files in a new atlases/subdirectory in /lh and /rh subfolders (or /mixed if you only have one file for lh and rh together). It should then pop up in the toolbox automatically.

Hope this helps!

Andy

[andreashorn]

Hi everybody,

in the future, please open up a new discussion for each question, otherwise, this might get a little difficult to read later on!

Thanks!
Andy

[melanogaster]

Hello,

is a complete install of Matlab (all toolboxes) necessary for running LEAD-DBS? And is a special version of Matlab needed?

I’m asking because i got this error message in Matlab right after >> lead:

??? Error using ==> hgload at 53
invalid Figure file format

Error in ==> openfig at 72
[fig, savedvisible] = hgload(filename, struct(‘Visible’,’off’));

Error in ==> gui_mainfcn>local_openfig at 286
gui_hFigure = openfig(name, singleton, visible);

Error in ==> gui_mainfcn at 159
gui_hFigure = local_openfig(gui_State.gui_Name, gui_SingletonOpt, gui_Visible);

Error in ==> lead at 42
gui_mainfcn(gui_State, varargin{:});

Matlab version 7.9.0 on MAC OSX 10.11

[andreashorn]

Dear melanogaster,

This could actually result from a quite old version of Matlab (2009b) not recognizing figures made with a newer version (2015b). I am not sure about backward compatibilities.
To the best of my knowledge, lead dbs should run with anything ~2011 on and doesn’t need many toolboxes. statistics, image processing if any.
We try to develop lead using least possible toolboxes.

Best, Andy

[kristen.kanoff]

Hi Andreas,

I am attempting to use the group GUI to plot lead locations for several patients on one image. I set the directory to a folder labeled “STN.” Within this folder are individual patient folders containing the contents of their “out” directory. As soon as I do this, I get the following MATLAB warning:

Warning: ‘popupmenu’ control requires that ‘Value’ be an integer within String range
Control will not be rendered until all of its parameter values are valid

If I proceed from here to add a patient (which I do by selecting their entire subfolder), I get the following MATLAB error:
Index exceeds matrix dimensions.
Error in lead_group>refreshvifc (line 744)
M.stimparams(pt,side).usefiberset=M.stimparams(pt,side).usefiberset{M.ui.fiberspopup};
Error in lead_group>addptbutton_Callback (line 249)
refreshvifc(handles);
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(‘addptbutton_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

Any advice would be very much appreciated.

Thank you,

Kristen

[andreashorn]

Dear Kristen,

sorry for this bug since it has already been reported (need to fix it soon). A workaround is to download the group connectome found here (http://www.lead-dbs.org/?page_id=317) and install the files after unzipping them into the lead/fibers folder.
It’s just that at present lead_group needs these files for the UI elements to work properly.

Please let us know if other errors occur since lead_group is still a a bit buggy and not well tested by many users yet.

Best, Andy

[macbeth83]

HI all. Thank you for the wonderful software!
I have a quick question: when I normalize to MNI the preoperative and postoperative MRI outside LeadDBS (I used SPM) I have two .nii files that I then rename correctly . When I start the reconstruction process though it gives an error saying that a

file y_ea_normparams.nii is missing

(I don’t have this file because I didn’t do the coregistration using LeadBDBS).
Do you have any idea on how to overcome this? I’m using MATLAB 2013b.

Thank you.

Best

[andreashorn]

Hi macbeth83,

this used to work in the past but in the novel versions, Lead-DBS performs reconstructions hybridly within patient and MNI space. Thus, a file that warps from subject to MNI space is needed. However, it doesn’t need to be an SPM file, ANTs is also supported. With which software did you normalize your data? Maybe the deformation file mapping from subject to MNI is similarly structured than y_ files or ANTs normalization parameters and we can figure out a workaround for you?

Best, Andy

[andreashorn]

Sorry just saw that you used SPM for the normalization. I think in this case you can just use the y_* file that SPM outputs for this (just make a copy and rename it to y_ea_normparams.nii – should work.

[macbeth83]

Thank you now it works!
Last question: I am following the instructions regarding the accumbens segmentation from a previous topic.
Shall I align the oxford atlas template from fsl to mni_hires.nii template from leaddbs folder before running the registration? Where can I find the routines in matlab that control the process of 2D/3D atlas visualization?

Thank you again.

[Author]

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