[Simnibs-discuss] T2 imaging protocol questions

[Valerie Nicolson]

Thanks so much for your answer!

We would be using a T1w with the T2-flair. When I ran headreco with both
the headmodel looked very good, but wasn't sure what errors I might
introduce by using the T2-flair instead of a T2.

Valerie

On Mon, Apr 5, 2021 at 11:26 PM Oula <oulap at drcmr.dk> wrote:

> 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.
>
>
>
> Best,
> Oula
>
>
>
> *Lähettäjä: *Valerie Nicolson <mrsnicolson at gmail.com>
> *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?
>
>
>
> Thanks,
>
>
>
> Valerie Cardenas Nicolson
>
> Palo Alto VA
>
>
>
>
>
>
>
>
>
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