What MRI is needed for normalization (reconstruction)?

[tsieger]

Hi,
please, is it possible to perform normalization and reconstruction using only one type of pre-operative MRI (e.g. coronal images) and one kind of post-operative MRI (e.g. transversal images), or is there a need to use all of (or at least two of) transversal, coronal, and sagittal post-operative MRI?

In my scenario, when I’m using pre-operative coronal MRI and post-operative transversal MRI, LeadDBS keeps saying:

Unnormalized MR-volumes found. Set normalize option.

in the status lower-left part of GUI even after normalization.

Does this mean that normalization did not succeed?

Looking in the ea_checkctmrpresent.m, it seems that LeadDBS expects both the transversal and coronal MRI for proper normalization, otherwise it will never report "Normalized MR-volumes found.":

if exist([uipatdir{1},filesep,prefs.tranii],'file') && exist([uipatdir{1},filesep,prefs.cornii],'file')
    try
    load([uipatdir{1},filesep,'ea_normmethod_applied.mat'])
    nmused=eval([norm_method_applied,'(''check'')']);
try    set(handles.statusone,'String',['MR-volumes have been normalized with: ',nmused]); end
    catch
try    set(handles.statusone,'String','Normalized MR-volumes found.'); end
    end
    modality(1)=1;
end

Thanks for clarification.

Best,
Tomas

[andreashorn]

Hi Tomas,

it is definitely possible to use only one.
If so, call the preop anat_*.nii (e.g. anat_t1.nii or anat_t2.nii or anat_pd.nii) and the postoperative one postop_tra.nii (no matter if it’s transversal, coronar or whatelse. The postop_tra.nii is the only needed file and if there is only one, one should call it that way.
It could well be that the status bar is outdated – so never mind what it says. I never pay attention to it much so it could be that the code that controls it is not correct anymore.

Best, Andy

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