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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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