For whatever reason, sometimes the T2w surface adjustment will be way off. Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit up and down can get it out of the minimum and make it work, so there might be a bug.
Matt.
Dear Bruce,
thank you for your help.
attached I have put an fslview, tkmedit screen-shot of the T2 image and a tksurfer image of lh.woT2.pial.
It appears that without consideration of the T2 this effect does not happen.
What would be your recommendation if I would like to keep using the T2 weighted image?
Yours,
Emil
Hi Emil
how do the surfaces look before you apply the T2 deformation? And how do
they look visualized over the T2 instead of the T1?
cheers
Bruce
On Thu, 8 May 2014, Emil H.J. Nijhuis
wrote:
Hi,
I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm
isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio
scanner with a 32-channel head coil. Unfortunately for half of my subjects I
receive an rather odd pial surface artefact, while the 'white' surfaces do
not suffer from the same issue.
The command line I have used was:
recon-all -all -subjid <subjectid> -T2 <subjectdir>/mri/orig/T2.mgz -T2pial
-3T
Are you familiar with this issue and do you have some advice for me?
Thank you very much for your help.
Yours sincerely,
Emil
--
----------------------------------------------
Emil H.J. Nijhuis, PhD
Researcher - Division of Diagnostic and Interventional Neuroradiology
University Hospital Basel
Petersgraben 4
CH 4031 Basel Switzerland
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