Viewing 2 posts - 1 through 2 (of 2 total)
Viewing 2 posts - 1 through 2 (of 2 total)
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Tagged: normalization
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
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It could well be that the status bar is outdated – so never mind what it says.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