[RafDM]

Hi Andy,
Thank you so much for this useful answer.
It seemed relatively easy, but I have tried in different way and I have obtained whenever the same error:
Error using spm_vol>spm_vol_hdr (line 80)
File “/home/***/Documents/DBS_dystonia/practice/pat_5/stimulations/gs_20180110144432/vat_right.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_exportvatmapping (line 28)
Vvatr=ea_load_nii([M.patient.list{pt},filesep,’stimulations’,filesep,’gs_’,M.guid,filesep,’vat_right.nii’]);

Error in lead_group>vizbutton_Callback (line 417)
ea_exportvatmapping(M,options,handles);

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

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

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

I don´t really know why it gives this error. I checked in the patient folder and that VTA is normally present.
Thereafter It happens for each patients that the process considers as first.

I´d be grateful if you could give an answer to the problem.
Kind regards, Raf

[RafDM]

Hi Andy,
Many Thanks for your answer.

FA template is not contained in the package (only T1, T2 and PD).
However, I renamed these nifti files accordingly with those present in default template but I cannot check normalization in detail and pre-reconstruction gave me this error:
Running job #4
————————————————————————
Running ‘Image Calculator’

SPM12: spm_imcalc (v6961) 16:47:16 – 09/01/2018
========================================================================
Failed ‘Image Calculator’
Error using spm_vol>spm_vol_hdr (line 80)
File “/_/_/LeadDBS/templates/space/MNI_NIHPD/bb.nii” does not exist.
In file “/home/_/spm12/spm_vol.m” (v5958), function “spm_vol_hdr” at line 80.
In file “/home/_/spm12/spm_vol.m” (v5958), function “spm_vol” at line 61.
In file “/home/_/spm12/spm_imcalc.m” (v6961), function “spm_imcalc” at line 101.
In file “/home/_/spm12/config/spm_cfg_imcalc.m” (v7216), function “my_spm_imcalc” at line 232.

The following modules did not run:
Failed: Image Calculator
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 #4
——————
Error while evaluating UIControl Callback

Then I have tried to copy/paste bb.nii in the folder of this new template.
Could this create a bias? (in the MNI_NIHPD package are contained only t1w, t2w, pdw, wm, gm, csf)

At this point I obtained different images of CT artifact: correct for left electrode and completely wrong for the right one.
I have encountered the same problem when I tried in the default template.
The weird thing is that it happened when I normalized with ANTs (both SyN or BsplineSyN) but not with three-steps affine normalization (coregistration with ANTs, they are preoperative T1 and postoperative CT)
Do you know what is the problem?

Thank you for your help and availability
Kind regards

[Author]

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