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Problem during Normalization

You are here: Home1 / Forums2 / Support forum ARCHIVED – Please use Slack Channel instead3 / Problem during Normalization4
Viewing 12 posts - 1 through 12 (of 12 total)
  • Author
    Posts
  • 05/20/2017 at 2:51 PM #2622
    mmendonca
    Participant

    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

    05/20/2017 at 5:33 PM #2623
    ningfei
    Keymaster

    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

    05/20/2017 at 11:22 PM #2625
    mmendonca
    Participant

    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

    05/21/2017 at 1:01 PM #2626
    mmendonca
    Participant

    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

    05/22/2017 at 7:54 AM #2630
    ningfei
    Keymaster

    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

    05/22/2017 at 9:44 AM #2632
    ningfei
    Keymaster

    Hi Marcelo,

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

    Best,
    Ningfei

    05/24/2017 at 9:36 AM #2647
    mike
    Participant

    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

    05/24/2017 at 10:30 AM #2648
    ningfei
    Keymaster

    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

    05/24/2017 at 6:35 PM #2652
    mike
    Participant

    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

    05/24/2017 at 7:40 PM #2653
    ningfei
    Keymaster

    Hi Mike,

    I just send you an email :)

    Best,
    Ningfe

    05/29/2017 at 10:37 AM #2667
    ningfei
    Keymaster

    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

    05/29/2017 at 8:32 PM #2673
    mmendonca
    Participant

    Hey Nigfei,
    Thanks for your help.

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

    Cheers,
    Marcelo

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