anat.nii file

[ggilmoreParticipant]

When making the anat.nii file which plane do I use? I have an axial plane and a coronal plane from a T1 and T2 weighted scan

I am using dcm2niix to convert the DICOM into nii files. Which format do I export in?

Greydon

[andreashornKeymaster]

Hi Greydon,

I’d advise to use a full-brain image with the best resolution available. If you have a highres full brain T2, maybe use this one since it shows the STN. Planes don’t really matter, it should be as high-res in all dimensions as possible (I guess an optimal file could e.g. be a 1x1x1mm T2 or T1).
If you use a T1, please name it anat_t1.nii in order that Lead-DBS uses the T1-MNI template for normalizations (this only works with ANTs).

dcm2nii is the optimal choice, please export the files in 4D nifti format (.nii ending).

Best, Andy

[ggilmoreParticipant]

Hi Andy,

I am still having issues with anatomy file. I have a coronal T2 weighted MR scan and have converted into 4D nifti. However, it stills gives me an error in Matlab “use suitable anatomy file”.

What are my options,

Greydon

[Author]

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