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Today's Topics:
1. v5.2.0 beta, round two (Nick Schmansky)
2. Re: pial not computing (Borzello, Mia)
3. Re: pial not computing (Bruce Fischl)
4. Re: FW: longitudinal analysis (Alex Hanganu)
---------- Forwarded message ----------
From: Nick Schmansky <nicks@nmr.mgh.harvard.edu>
To: <freesurfer@nmr.mgh.harvard.edu>
Cc:
Date: Fri, 18 Jan 2013 11:20:43 -0500
Subject: [Freesurfer] v5.2.0 beta, round two
For those willing and brave enough, another beta of v5.2.0 has been posted
here for you to download and test:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
The Mac builds should work (note: the lion build is 64b, snow-leopard is
32b).
The final release still awaits some critical improvements to the Tracula
stream, but the main recon-all stream with this beta is final. The final
release is expected the first week of February.
Freesurfer team
---------- Forwarded message ----------
From: "Borzello, Mia" <MBORZELLO@partners.org>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc:
Date: Fri, 18 Jan 2013 16:25:40 +0000
Subject: Re: [Freesurfer] pial not computing
great. is there a freesurfer page on mris_topo_fixer? I'm not sure how/where to run this and I don't see a page on the freesurfer site.
Thanks so much,
m
________________________________________
From: Bruce Fischl [fischl@nmr.mgh.harvard.edu]
Sent: Thursday, January 17, 2013 1:30 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new mris_topo_fixer
and you rerun and it should be all set. You probably should take a look
at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum
or skull attached, and the hemispherees successfully separated)
cheers
Bruce
On Thu, 17
Jan 2013, Borzello, Mia wrote:
> Okay, so it didn't complete without error. I've attached the recon-all.log. Also, I was using another post op patient's MRI scans.
>
> thanks so much,
> m
> ________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu]
> Sent: Thursday, January 17, 2013 11:22 AM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] pial not computing
>
> Hi Mia
>
> we need to see the recon-all.log. Did it end with an error?
> Bruce
> On Thu, 17 Jan
> 2013, Borzello, Mia wrote:
>
>> Hi Freesurfers,
>>
>> I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this?
>> Thanks,
>> m
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------- Forwarded message ----------
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
To: "Borzello, Mia" <MBORZELLO@partners.org>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Date: Fri, 18 Jan 2013 11:28:00 -0500
Subject: Re: [Freesurfer] pial not computing
it's run as part of recon-all. If you grab a new one and run
recon-all -make all ...
you should be all set
Bruce
On Fri, 18 Jan 2013, Borzello, Mia wrote:
great. is there a freesurfer page on mris_topo_fixer? I'm not sure how/where to run this and I don't see a page on the freesurfer site.
Thanks so much,
m
________________________________________
From: Bruce Fischl [fischl@nmr.mgh.harvard.edu]
Sent: Thursday, January 17, 2013 1:30 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new mris_topo_fixer
and you rerun and it should be all set. You probably should take a look
at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum
or skull attached, and the hemispherees successfully separated)
cheers
Bruce
On Thu, 17
Jan 2013, Borzello, Mia wrote:
Okay, so it didn't complete without error. I've attached the recon-all.log. Also, I was using another post op patient's MRI scans.
thanks so much,
m
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu]
Sent: Thursday, January 17, 2013 11:22 AM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] pial not computing
Hi Mia
we need to see the recon-all.log. Did it end with an error?
Bruce
On Thu, 17 Jan
2013, Borzello, Mia wrote:
Hi Freesurfers,_______________________________________________
I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this?
Thanks,
m
_______________________________________________
Freesurfer mailing list
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---------- Forwarded message ----------
From: Alex Hanganu <al.hanganu@yahoo.ca>
To: FS Mailing List <Freesurfer@nmr.mgh.harvard.edu>
Cc:
Date: Fri, 18 Jan 2013 11:39:31 -0500
Subject: Re: [Freesurfer] FW: longitudinal analysis
Hi Paul,
I also had such problems previously. My initial analyses were performed on mac. Though it might seem strange, some analyses resolved after I just restarted the computer. Other ones I analysed on centos. Now I am doing all the recons on linux.
best wishes,
Alex.
Le 1/18 9:22, paul horton a écrit :
> Date: Fri, 18 Jan 2013 08:54:48 -0500
> From: fischl@nmr.mgh.harvard.edu
> To: horton_paul@hotmail.com
> Subject: RE: [Freesurfer] longitudinal analysis
>
> Hi Paul
>
> can you cc the list so that others can answer?
>
> thanks
> Bruce
> On Fri, 18 Jan 2013, paul
> horton wrote:
>
> > Hi Brian,
> >
> > Thanks for your reply.
> >
> > I am running freesurfer 4.5.0. We are using the older version so that the
> > analyses performed are the same across subjects.
> >
> > Best wishes
> >
> > Paul
> >
> > Date: Fri, 18 Jan 2013 08:21:05 -0500
> > From: fischl@nmr.mgh.harvard.edu
> > To: horton_paul@hotmail.com
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] longitudinal analysis
> >
> > Hi Paul
> >
> > what is the actual binary being run?
> >
> > Bruce
> > On Fri, 18 Jan 2013, paul horton wrote:
> >
> > > Hi guys,
> > >
> > > I am currently running a longitudinal analysis on a set of scan. It is
> > > currently running and so far it has taken 5 days. It seems to be taking a
> > > large amount of time on a process called labelling slice. I have run the
> > > same analysis on other subjects which took about 6 hours to complete. So
> > I
> > > was wondering if you know of any reason why a set of scans would take long
> > er
> > > to process than others. I have checked the inital scans and nothing seems
> > > obviously wrong with them.
> > >
> > > Best Wishes
> > >
> > > Paul
> > >
> > >
> >
> > _______________________________________________ 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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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.