Dear Dr. Fischl,

Thanks for your quick reply.

Attached you will find some images showing the issues we're having.

The images are as follows:

1.) sagittal_1353_norm2+3T_vs_default -> the v5.3 suggested norm2 flags (from the release notes) and the -3T flag vs. the default v5.3 pipeline. Blue is the norm2/3T flag pipeline, yellow is the default.

2.) sagittal_1353_wusl_vs_default ->v5.3 using the -washu_mprage flag, obvious improvement in temporal lobe pial surface. Blue is -washu_mprage flag, yellow is the default v5.3 pipeline

3.) axial_1353_norm2+3T_white -> The white surface, which appears OK using v5.3 with the suggested norm2 parameters and the -3T flag

4.) axial_1353_wusl_white_error -> the white surface, with an obvious error in the lh_postcentral area, using the -washu_mprage flag.

Let me know if you have any suggestions on other parameters I should try to improve the temporal lobe pial surface, without compromising the white matter surface reconstruction.

Sincerely,

Las

Message: 5 Date: Mon, 7 Jul 2014 11:14:25 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Anterior Temporal Lobe / Pial Reconstruction Troubles To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1407071114090.30923@nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Hi Las

can you send us a couple of images of the problems you are seeing?

cheers Bruce On Mon, 7 Jul 2014, Las Blawimo wrote:

Dear FreeSurfer Experts,

We are collecting a 0.9mm isotropic FSPGR sequence on a GE MR750 3T

scanner.

We're observing, in many subjects, a problem mentioned in previous posts

to

the list where the pial surface does not follow the cortex properly in the anterior temporal lobe region (and also in some frontal regions). The

white

matter surface generally looks very good. This is with the default options from recon-all in v5.3.

We've also tried running the following options, based on previous posts (expert options) and the release notes for version 5.2:

-norm2-b 20 -norm2-n 5

and

-norm2-b 20 -norm2-n 5 -3T

In general, there is a modest improvement in the medial temporal lobe pial surface in most subjects. A substantial/desired improvement is observed in only a few subjects. In general, there was no detrimental effect to either the white matter or pial surface when using these flags.

Based on older posts to the list, we've also tried using the following flags:

-mprage

and

-washu_mprage

The improvement to the pial surface is much more substantial in almost all subjects, to some extent with the -mprage flag, mostly with the -washu_mprage flag. However, this dramatic improvement in pial surface accuracy was accompanied by many major issues with the white surface in widespread areas across the brain. Also, some subjects fail to reconstruct fully due to large defects in the surfaces with this option in place (also something I've read about happening to people using the -washu otpion on

the

list).

A few questions:

Would you suggest we also try the options "-norm1-b" and "-norm1-n" in addition to the norm2 options? If so, any suggested starting values to

try?

Alternatively, would it be sensible to try to use the white surface from

the

default pipeline and combine it with (or perhaps initialize) the pial surface from the -washu_mprage flag?

Do you have other suggestions for us to try?

Thank you for your time and help!

Sincerely,

Las