[Simnibs-discuss] T2 imaging protocol questions

Oula oulap at drcmr.dk
Tue Apr 6 08:19:27 CEST 2021

Hi Valerie,

If you’re planning to skip a T1w scan completely the answer is yes and no. You can create a headmodel with headreco using a FLAIR, and that will likely turn out fairly okay, but you cannot use the CAT12 toolbox (included in headreco) to create the middle cortical surface. CAT12 requires a T1 in order to work. So if you need the middle cortical surface to visualize the electric field or mapping onto the FreeSurfer average space then you should have a T1w scan.

W.r.t. the T1/T2 it’s exactly as you described: the field-of-view is cropped to the smaller scan. So if the T2 only had the upper part of the head, the T1 will be masked to also only have the upper part of the head, and the masked/missing part is reconstructed from the template.


Lähettäjä: Valerie Nicolson
Lähetetty: 2. april 2021 09:42
Vastaanottaja: discuss at simnibs.org
Aihe: [Simnibs-discuss] T2 imaging protocol questions

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

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