Problem during Normalization

[mmendonca]

Hey guys,
I am a new user of Lead-DBS and I have been trying to localize the electrodes. I have a post-op CT scan, and a pre-op MRI (with T1, T2 and DP).
After importation to nift and co-registering the CT with the MR, i am not able to run the normalization. I get the following errors.
Any idea?

Tonemapping CT…
Error using spm_vol>spm_vol_hdr (line 80)
File “C:\MATLAB\RafPinto\Rafa_NewTry\DICOM_MR\glpostop_ct.nii” does not exist.

Error in spm_vol (line 61)
v = spm_vol_hdr(deblank(P(i,:)));

Error in ea_load_nii (line 28)
nii=spm_vol(fname);

Error in ea_tonemapct_file (line 19)
ct=ea_load_nii([directory,options.prefs.gctnii]);

Error in ea_autocoord (line 97)
ea_tonemapct_file(options,’mni’);

Error in ea_run (line 95)
ea_autocoord(options);

Error in lead_dbs>run_button_Callback (line 190)
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

[ningfei]

Hi,

ea_tonemapct_file is called after the normalization is done. If you saw the above error. It means that the normalization step did not finish correctly. Please check the log before the error to see if there is something wrong there.

Best,
Ningfei

[mmendonca]

Hey ningfei, Thanks for the fast answer
I will rerun the normalization and tell you the details (i did not saved the log)

Thanks,
Marcelo

[mmendonca]

Hey ningfei;
Heres is the full error I get:

Exception Object caught:

itk::ExceptionObject (00000050A82FCF18)
Location: “unknown”
File: c:\users\ningfei\desktop\ants\bypass\itkv4-install\include\itk-4.11\itkImageToImageFilter.hxx
Line: 250
Description: itk::ERROR: ImageToImageFilter(000001CA4E20C7E0): Inputs do not occupy the same physical space!
InputImage Origin: [9.7750000e+01, 1.3375000e+02, -7.1750000e+01], InputImage_1 Origin: [9.8000000e+01, 1.3400000e+02, -7.2000000e+01]
Tolerance: 1.0000000e-06
InputImage Spacing: [1.0000000e+00, 1.0000000e+00, 1.0000000e+00], InputImage_1 Spacing: [5.0000000e-01, 5.0000000e-01, 5.0000000e-01]
Tolerance: 1.0000000e-06

Using single precision for computations.
Input scalar image: C:\MATLAB\RafPinto\Rafa_NewTry\DICOM_MR\anat_t1.nii
Reference image: C:\Users\marce\Downloads\lead\templates\space\MNI_ICBM_2009b_NLIN_ASYM\t1.nii
Transform file does not exist: C:\MATLAB\RafPinto\Rafa_NewTry\DICOM_MR\glanatComposite.h5
Can’t read initial transform C:\MATLAB\RafPinto\Rafa_NewTry\DICOM_MR\glanatComposite.h5
Using single precision for computations.
Input scalar image: C:\MATLAB\RafPinto\Rafa_NewTry\DICOM_MR\rpostop_ct.nii
Reference image: C:\Users\marce\Downloads\lead\templates\space\MNI_ICBM_2009b_NLIN_ASYM\t1.nii
Transform file does not exist: C:\MATLAB\RafPinto\Rafa_NewTry\DICOM_MR\glanatComposite.h5
Can’t read initial transform C:\MATLAB\RafPinto\Rafa_NewTry\DICOM_MR\glanatComposite.h5
C:\MATLAB\RafPinto\Rafa_NewTry\DICOM_MR\glanat.nii not found. Skip generating l*.nii files (small bounding box)…
C:\MATLAB\RafPinto\Rafa_NewTry\DICOM_MR\glpostop_ct.nii not found. Skip generating l*.nii files (small bounding box)… Done. (80100.3978 s)
Tonemapping CT…
Error using spm_vol>spm_vol_hdr (line 80)
File “C:\MATLAB\RafPinto\Rafa_NewTry\DICOM_MR\glpostop_ct.nii” does not exist.

Any idea/suggestion?

Thanks
Marcelo

[ningfei]

Hi Marcelo,

Seems it’s possibly an known issue of ITK which is used by ANTs. I will check it later and maybe there’re some ways to work around it.

Best,
Ningfei

[ningfei]

Hi Marcelo,

Please extract this into lead\ext_libs\ANTs (overwrite the old ones) and try again to see if it works.

Best,
Ningfei

[mike]

Hi,

Sorry to crash this thread but I am in exactly the same situation. I’ve tried the advice above (regarding extracting new files into ANTs and overwriting the old ones) and I still end up with the same error.

Any advice to help fix this would be most appreciated.

Best wishes,
Mike

[ningfei]

HI Mike,

Sorry to know that you also have the problem. But since I can’t reproduce the problem from my side, it would be nice if you can send me a sample data with which you got the above error (of course if it’s okay to share the data). I may then test it here to find a possible solution for that.

Best,
Ningfei

[mike]

Hi Ningfei,

Many thanks for the quick reply. Yes I can share data, just let me know the best way to do this. You should have my personal email through the account information so feel free to contact me that way if it’s easier.

Best,
Mike

[ningfei]

Hi Mike,

I just send you an email :)

Best,
Ningfe

[ningfei]

Hi Mike, hi Marcelo,

According to my test, here the error “Inputs do not occupy the same physical space!” was induced due to insufficient memory (to me, this is really weird). The last two steps of the (ANTs Syn – subcortical refine) normalization require significant amount of memory. I also saw this error when I tested on my pc with 16GB memory. But there’s no problem when I tested it on our server with very large memory.

Actually, the registration is already done when the error happens. But the memory is not released somehow. ANTs will throw out the error when further generating the composite transforms.

This error doesn’t happen when using ANTs Syn normalization without subcortical refine.

In short, could you maybe test it on a machine/cluster with above 24GB (or better 32GB) memory to see if this error still exists? I will also check the parameter setting and ANTs code to see if there’s any clue on this.

Best,
Ningfei

[mmendonca]

Hey Nigfei,
Thanks for your help.

I will try it in our cluster and then tell you something

Cheers,
Marcelo

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