Hi Areti
at the moment there is no official beta for V6, since we effectively recalled it. It will induce differences and variance into your study. An alternative would be to just rerun all of your subjects (preserving all manual edits) in V6 when it is finally out. Otherwise you will need to make sure that these subjects are balanced in your study (i.e. that they are not all controls or patients or whatever)
cheers Bruce
On Thu, 10 Mar 2016, Smaragdi A. wrote:
Hi mailing list,
regarding a previous issue with the v5.3.0 and the pial boundary crossing into the ventricles (below), i have run the subjects in the beta version and the problem does not appear.
My question to the experts is now, considering it is not advised to switch versions in a data set, how 'bad' would it be to run 7 subjects in the beta version, and the other 190 or so in the v5.3.0 version?
It is after all a very small number of the total sample, would this be ok, or would you still advise against it?
Many thanks,
Areti
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Smaragdi A. [A.Smaragdi@soton.ac.uk] Sent: 12 January 2016 18:27 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject)
Hi Bruce,
thanks for the quick reply, I am running v5.3.0 from a Linux, but more than 2/3 through my data set so don't really want to swap to 6..
Where can I get the beta and how would it help?
Thanks,
Areti
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 12 January 2016 16:24 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject)
what version are you running? I believe that this is a bug that has been fixed. Hopefully we will get version 6 out soon and upgrading will fix this, but you can download a beta and try to make sure if you want
cheers Bruce On Tue, 12 Jan 2016, Smaragdi A. wrote:
Hi mailing list,
I have encountered this problem in Freesurfer a number of times now and I wondered if any of you had any solutions.
It seems that sometimes after a recon-all has been run, there is a large overlap of the pial boundary and wm boundary, in the same region each time near the lateral ventricles (it can be on either hemisphere or both). I have attached a print screen of the issue, this time in the LH. As you can see, we have tried adding CPs and have also added WM, but after re-running it, the problem still exists. We have also tried running the randomness, but this has had no effect.
Any suggestions as to what we could do to fix this would be great - thank you!
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