DTI Analysis

[marucela]

Good morning Lead DBS Team,
We are working with the lead dbs, our data are: Postop CT (No contrast 1mm), pre-op MRI T2 (1.3mm), DTI (Ideally 4 or less mm). Our final goal is to analyze and visualize the fibers that pass through the stimulated area for which we have used the following pipeline:
1. Coregistration
2. Normalization (with the SPM12 segment nonlinear method)
3. Reconstruction of Electrode Trajectories
4. Visualization: the simulation of stimulation was carried out and a “vat_seed_compound_dMRI_struct_seed.nii” file was generated inside the stimulations folder.
5. Perform connectivity analyzes: running “lead connectome” has generated, in the patient’s directory:
• two folders: connectomes and connectomics
• within the stimulations folder, it was generated 2 empty folders: No structural connectome found and Patient-specific fiber tracs.
6. Lead connectome mapper, we run this step with the seed generated from the simulation of stimulation, and in step 2 “Connectome definition-Include structural (dMRI) connectivity”, there is the message “No structural connectome found”; with which when running the lead connectome mapper we get error.
Please, could anyone help us with this?
Thanks in advance,
Marucela.

[ningfei]

Hi Marucela,

What’s the full path of your patient folder? What’s insides the folder connectomes/dMRI under patient folder? And your LEAD version?

Best,
Ningfei

[marucela]

Dear Ningfei,
Thank you very much for your prompt response.

The path of my patient is: /home/gabriel/Desktop/GrilloAN
Iinsides the folder connectomes/dMRI under patient folder, I have:
wFTR.mat
wFTR.tkr
wFTR_vox.mat
The version of the Lead DBS that I am using is: v2.1.5

My best regards,

Marucela.

[ningfei]

Dear Marucela,

The connectome folder looks in order. There should be an option Patient-specific fiber tracts inside the popup menu under Include structural (dMRI) connectivity. But it’s missing now, isn’t it? What’s the output of ea_genmodlist if you run it in the MATLAB command window?

Maybe you can also try to install the hotfix from here, which would update your lead-dbs to the development version. And see if the error still occurs. If so, you may send me some screenshots via Slack (join our Slack group here if you are not in it yet).

Best,
Ningfei

[marucela]

Dear Ningfei,
When I run the ea_genmodlist command, what comes up is the following:
>> ea_genmodlist

ans =

0×0 empty cell array

The option Patient-specific fiber tracts does not appear by default, it only appears when I manually enter the patient’s folder in “specify/Patient”, with which I must choose the seed manually in “Seed Output definition”, which results in this is:
Warning: No anatomy information found! Please put either anat_t1.nii, anat_t2.nii or anat_pd.nii into subject
folder.
> In ea_assignpretra (line 16)
In ea_autocoord (line 76)
In ea_run (line 96)
In lead_mapper>run_button_Callback (line 241)
In gui_mainfcn (line 95)
In lead_mapper (line 42)
In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_mapper(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
Index exceeds array bounds.

Error in ea_autocoord (line 89)
if ~exist([directory,’raw_’,presentfiles{1}],’file’)

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

Error in lead_mapper>run_button_Callback (line 241)
ea_run(‘run’,options);

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

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

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_mapper(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.

However, in the patient’s folder we have anatomical information, we have the file anat_t2.nii
But, we do not understand why we get the errors that you can see in the screenshot
I will reinstall the Lead Dbs and run all the steps for our project, and I will update you on the results through the slack in which I will join now.
Just in case, we are using the linux ubuntu 16.04 lts
Thank you so much!
Marucela.

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