[Vinny]

Thanks Andy!

Cheers/Vinny

[Vinny]

Hi Ningfei,

I downloaded and extracted to lead folder. I now have version 1.6.4.2.

Thanks again for your help!
Vinny

[Vinny]

Hi Ningfei,
I clicked on the link to the updated package but the file was removed. Would it be possible if you could send it again?
Thanks,
Vinny

[Vinny]

Thanks Ningfei!
Regards,
Vinny

[Vinny]

Hi Ningfei,
As recommended, I exited the developer version by setting prefs.env.dev= 0. I have lead-DBS version 1.6.4.1.

[Vinny]

Just fyi, will retry later :)

[Vinny]

Thanks Andy!

[Vinny]

Thanks Andy and Ningfei, it works great!

Best,
Vinny

[Vinny]

Hi,
I had applied the latest update, ie, today, and ran ANTs normalization for the nonlinear registration step. Please note the following error message. Thanks.
Vinny

Error using eval
Undefined function or variable ‘ea_antspreset_SyN_default’.
Error in ea_ants_nonlinear (line 84)
apref=eval(funname);
Error in ea_normalize_ants (line 79)
ea_ants_nonlinear(to,from,[directory,options.prefs.gprenii],weights,options,options.prefs.machine.normsettings.ants_scrf);
Error in ea_autocoord (line 94)
eval([options.normalize.method,'(options)’]); % triggers the normalization
function and passes the options struct to it.
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

[Vinny]

Hi Andy,

Not a problem and thanks for your help. I’ll try on my lab computer with a larger RAM but will also wait for the new version to be released. The normalization is pretty good with the SPM12 DARTEL nonlinear procedure though.

Kind regards,
Vinny

[Vinny]

Hi Ningfei,
I had suspected a memory issue as well but wanted to make sure since ANTs SyN had worked on my laptop prior to the update. How do I access the development version of lead? Do I have to modify the ea_prefs file? Thank you very much for your help,

Kind regards,
Vinit

[Vinny]

Thanks Andy

[Vinny]

Hi Andy,

I tested Lead-Connectome with diffusion-weighted imaging data from BrainSuite and was able to complete all the steps and obtain the DTI connectivity matrix. For the BrainSuite data, the extensions are .bval and .bvec as opposed to the .txt extension from the HCP for the bval and bvec files. Also, I had renamed from diff.nii to dti.nii and re-ran the HCP data but the same error appeared after trying to export FA. I am not sure if the .txt extension is the issue.

Regards/Vinit

[Vinny]

Thanks Andy. I’ve bolded the subset of files from HCP that I’m using for Lead-Connectome:

anat/ Anatomical scans
T1/T1.nii.gz MPRAGE
T2/T2.nii.gz T2-weighted

diff/ Diffusion scans
raw/ unprocessed data
mri/diff.nii.gz four shells, b-values of b1k, b3k, b5k, and b10k
bvals.txt b-values
bvecs.txt diffusion gradient directions
bvecs_fsl.txt FSL compatible version of diffusion gradient directions

I renamed the files to be compatible for reading by Lead-Connectome but get the error message that the dti.bval file is unable to be read. Is it because the bvec and bval files are in .txt extension rather than .bvec and .bval format?

*** Performing structural parts of LEAD-Connectome…
Building DTI files…
Export b0…
Error using load
Unable to read file ‘C:\Users\Vinit\Documents\MATLAB\Diffusion-raw\dti.bval’. No such file or directory.
Error in ea_exportb0 (line 4)
bvals=load([options.root,options.patientname,filesep,options.prefs.bval]);
Error in ea_prepare_dti (line 14)
ea_exportb0(options);
Error in ea_ft_gqi_yeh (line 13)
ea_prepare_dti(options)
Error in ea_perform_ft_proxy (line 6)
eval([options.lc.struc.ft.method,'(options)’]); % triggers the fibertracking function and passes the options
struct to it.
Error in ea_perform_lc (line 13)
ea_perform_ft_proxy(options);
Error in ea_autocoord (line 109)
ea_perform_lc(options);
Error in ea_run (line 95)
ea_autocoord(options);
Error in lead_connectome>runsavebutn_Callback (line 289)
ea_run(‘run’,options);
Error in gui_mainfcn (line 95)
feval(varargin{:});
Error in lead_connectome (line 42)
gui_mainfcn(gui_State, varargin{:});
Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_connectome(‘runsavebutn_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

[Vinny]

Hi Ningfei,

I downloaded Lead-DBS on Feb 10, 2017 and it was version 1.6.2. I upgraded to version 1.6.3 and have the brainshift correction feature installed. Thanks for the sending the pca.nii file; I placed it in the appropriate subfolder in the lead folder. However, now I get a new error message when assessing structural connectivity using deterministic fibertracking related to no b0.nii file existing; diff.nii, dti.bval, dti.bvec, and anat_t1 files exist in the patient folder.

Thanks/Vinit

Running job #1
————————————————————————
Running ‘Coregister: Estimate & Reslice’

SPM12: spm_coreg (v6435) 23:57:54 – 01/04/2017
========================================================================
Failed ‘Coregister: Estimate & Reslice’
Error using spm_vol>spm_vol_hdr (line 80)
File “C:\Users\Vinit\Documents\MATLAB\Diffusion-raw\b0.nii” does not exist.
In file “C:\Users\Vinit\Downloads\spm12\spm_vol.m” (v5958), function “spm_vol_hdr” at line 80.
In file “C:\Users\Vinit\Downloads\spm12\spm_vol.m” (v5958), function “spm_vol” at line 61.
In file “C:\Users\Vinit\Downloads\spm12\spm_coreg.m” (v6435), function “spm_coreg” at line 117.
In file “C:\Users\Vinit\Downloads\spm12\config\spm_run_coreg.m” (v5956), function “spm_run_coreg” at line 22.

The following modules did not run:
Failed: Coregister: Estimate & Reslice

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
——————
Error while evaluating UIControl Callback

[Author]

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