Dear Matt,
I do not use HCP pipeline scripts for this project.
This is standard 1x1x1 mm3 data so I thought standard freeSurfer pipeline could
work well here.
I also thought that standard recon-all version 6.0 with this data should work
better than v5.3 which, I expect, solved some issues with v5.3 (some of them I
was discussing in the forum previously):
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41880.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42312.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41375.html
But anyway, thank you for your feedback.
Antonin
Since I believe you said you are using my code, I would recommend to stick
with 5.3 at this time.Peace,
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Antonin Skoch
<a...@ikem.cz>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, February 7, 2017 at 2:59 PM
To: <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much
more externally in comparison to v5.3
Dear Bruce,
thank you for the feedback. I would definitely be interested in 6.1 beta.
What is the approximate timeline of release?
We are working on quite large project (involving -FLAIRpial) and I have to
decide whether to go to v6.0 or to stick with v5.3.
Do you think that so far the 5.3 version is better for T2/FLAIR? Why this is
the case?
Antonin
Hi Antonin
yes, V6 was not meant for T2/FLAIR and we didn't test it extensively. We
have been optimizing things in the past week for T2/FLAIR and I expect 6.1
will be better for them. We can give you a beta soon if you like.
cheers
Bruce
On Tue, 7
Feb 2017, Antonin Skoch wrote:
> Dear experts,
>
> I have reprocessed my groups of subjects (originally processed by v5.3) by
> v6.0. I am using -FLAIRpial for pial surface refinement.
>
> I have noticed that the pial surfaces in v6.0 after -FLAIRpial are positioned
> much more externally in comparison to -FLAIRpial in v5.3. The v6.0 version
> includes to pial sheet much more partial volume voxels in
> comparison to v5.3.
>
> In contrast to v5.3, where the surfaces after -FLAIRpial were mostly
> internally with respect to pial surfaces determined by T1, in v6.0 there are
> many regions where the pial surfaces after -FLAIRpial are placed
> much externally with respect to pial surfaces determined by T1.
>
> See the screenshot (red surfaces are pial surfaces after -FLAIRpial with
> v6.0, yellow are surfaces after -FLAIRpial with v.5.3).
>
> I have used -nsigma_above 8 in mris_make_surfaces to prevent excluding some
> cortical regions with high signal intensity but this I used consistently in
> both versions so it should not be the reason of difference.
>
> I have uploaded the subject processed both by 5.3 and 6.0 version to your
> server, files FLAIRpial_v5.3.tar.gz and FLAIRpial_v6.0.tar.gz.
>
> Could you please look at my data and check whether the pial surfaces after
> -FLAIRpial in v6.0 look OK from your perspective?
>
> Regards,
>
> Antonin Skoch
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