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