Does the beta permit volumes bigger than 256^3 voxels? just asking....and just asking about raw dimensions in unit-voxels at the start of pipeline
cheers
Colin
On 18 January 2013 17:00, freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- v5.2.0 beta, round two (Nick Schmansky)
- Re: pial not computing (Borzello, Mia)
- Re: pial not computing (Bruce Fischl)
- 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
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---------- 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.edufreesurfer-bounces@nmr.mgh.harvard.edu[ freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-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
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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
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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.