Probably Emil¹s current example would be best because it is failing in your recon-all setup.

Matt.

On 5/9/14, 9:31 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

Hi Matt

if you can send me an example I'll try to find time to take a look Bruce On Fri, 9 May 2014, Matt Glasser wrote:

...

Hi Bruce,

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.

Peace,

Matt.

From: "Emil H.J. Nijhuis" emil.nijhuis@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, May 9, 2014 at 4:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

Dear Bruce,

thank you for your help.

attached I have put an fslview, tkmedit screen-shot of the T2 image and a tk surfer 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 weigh ted 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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