Hi Josh
the way we are handling sub-mm data is to run it through the standard recon-all, then run a postprocessing surface deformation on the higher res data. Our preliminary results are pretty encouraging on T1s, T2s and FLAIRs.
cheers Bruce
On Mon, 21 Jan 2013, Joshua Lee wrote:
Does this mean that using Freesurfer at sub-1mm isotropic resolutions will not be possible next version? Josh
On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: Colin,
It will still error if any dimension is greater than 256, which then means the flag -cw256 must be added to recon-all. This flag chops dimensions greater than 256 down to 256. The reason it doesnt do it automatically is that with this chopping, its not certain that it isnt removing into the head, so the user needs to be aware of this, so that they can inspect orig.mgz with freeview to make sure the head is fully visible. Nick > 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: > >> Send Freesurfer mailing list submissions to >> freesurfer@nmr.mgh.harvard.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> or, via email, send a message with subject or body 'help' to >> freesurfer-request@nmr.mgh.harvard.edu >> >> You can reach the person managing the list at >> freesurfer-owner@nmr.mgh.harvard.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Freesurfer digest..." >> >> 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.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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