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(a)nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Anterior Temporal Lobe / Pial Reconstruction
Troubles
To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>
Message-ID: <alpine.LRH.2.03.1407071114090.30923(a)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
>
>