No slabs found

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  • 02/16/2018 at 12:02 PM #4192
    Nabkr
    Participant

    Dear Lead DBS team,
    Firstly, thanks for the update and Lead predict. But sadly there is an error again and could not exactly figure out the reason. Your help would be really appreciated. The error is during the coregistration, it says ‘ No slabs found in T1 image as shown below. I imported the Dicom and it seemed all good. But it gets stuck in this step always. I also tried converting the nifti by myself but still says the same. I checked the Dicom before and all seems good. Cant figure out.

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

    SPM12: spm_coreg (v6435) 11:51:19 – 16/02/2018
    ========================================================================
    Completed : 11:51:41 – 16/02/2018

    SPM12: spm_reslice (v7141) 11:51:41 – 16/02/2018
    ========================================================================
    Completed : 11:51:58 – 16/02/2018
    Done ‘Coregister: Estimate & Reslice’
    Done

    Including FA information for white-matter normalization.
    Including anat_t2.nii data for (grey-matter) normalization
    Including anat_t1.nii data for (grey-matter) normalization
    Checking for slabs among structural images (assuming dominant structural file C:\Users\e_n\Desktop\try_1\anat_t1.nii is a whole-brain acquisition)…
    No slabs found.
    Undefined function or variable ‘ea_antspreset_effective_lowvariance’.

    Error in ea_ants_nonlinear (line 88)
    apref = feval(eval([‘@’, options.prefs.machine.normsettings.ants_preset]), options.prefs.machine.normsettings);

    Error in ea_normalize_ants (line 80)
    ea_ants_nonlinear(to,from,[directory,options.prefs.gprenii],weights,options);

    Error in ea_autocoord (line 154)
    eval([options.normalize.method,'(options)’]); % triggers the normalization function and passes the
    options struct to it.

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

    Error in lead_dbs>run_button_Callback (line 187)
    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.

    Thank you.

    Regards,
    Nabin

    • This topic was modified 6 years, 9 months ago by Nabkr. Reason: Privacy protection of the patients detail
    02/16/2018 at 12:58 PM #4194
    ningfei
    Keymaster

    Hi Nabin,

    This is because the I changed the ANTs presets names. A simple solution would be:

    1. Open the ANTs Settings button (after the Normalization methods popup menu).
    2. Check the settings there, choose Effective: Low Varriance, Default
    3. Clike Save button.

    Try it again.

    Best,
    Ningfei

    02/16/2018 at 4:02 PM #4195
    Nabkr
    Participant

    Dear Ningfei,
    Thank you it worked after I changed the settings as you suggested. But now I got stuck in almost the last step. When I am trying to export 2D slices ouput, it says patient Pre-OP does not exists. Irrespective of the template or atlas I select. Am I missing something ?

    Exporting 2D slice output…
    Error using spm_vol>spm_vol_hdr (line 80)
    File “Patient Pre-OP” does not exist.

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

    Error in ea_assignbackdrop (line 105)
    varargout{1}=spm_vol(bdstring);

    Error in ea_writeplanes (line 69)
    [Vtra,Vcor,Vsag]=ea_assignbackdrop(options.d2.backdrop,options,’Patient’);

    Error in ea_write (line 48)
    cuts=ea_writeplanes(options);

    Error in ea_autocoord (line 257)
    ea_write(options)

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

    Error in lead_dbs>run_button_Callback (line 187)
    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.

    Thank you.

    Regards,
    Nabin

    02/16/2018 at 5:37 PM #4196
    ningfei
    Keymaster

    Dear Nabin,

    For that I guess it might be solved similarly. You could:

    1. Open the 2D Settings (after the Write out 2D check box).
    2. Choose the backdrop as you want (the first one is MNI T1 image, which is used by default).
    3. Click Save and close.

    Then try it again.

    Best,
    Ningfei

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