[Simnibs-discuss] T2 imaging protocol questions

Valerie Nicolson mrsnicolson at gmail.com
Thu Apr 1 20:36:24 CEST 2021

Hello all,

Can anyone advise on the suitability of using a high resolution 3D T2 Flair
sequence for headreco? A collaborator is already acquiring this in their
study, and the output of headreco looks good to me (though I am no expert),
and we are trying to figure out if they need to add a T2 to their protocol
if we want to do electric field modeling.

Also, on some older data, we have a low resolution T2 with brain coverage
(not full head/face coverage like the T1). The GM, WM, CSF segmentation
looks OK, but I get some very strange results for skin and bone. It looks
like the skin of the subject superiorly (where there was both T1 and T2
coverage) and the skin of the template elsewhere (where there was T1
coverage only...see attached picture). The T1 and T2 look registered (if I
compare T1fs_conform.nii.gz to T2_conform.nii.gz), and
T1fs_nu_nonlin_MNI.nii looks registered to MNI152_T1_1mm.nii (using
headreco check), but T1fs_nu_12DOF_MNI.nii is way off. Any thoughts?


Valerie Cardenas Nicolson
Palo Alto VA

[image: Screen Shot 2021-04-01 at 11.27.43 AM.png]
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