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-requ...@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-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@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 <ni...@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" <mborze...@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 [fis...@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-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ > fis...@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 <fis...@nmr.mgh.harvard.edu> > To: "Borzello, Mia" <mborze...@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 [fis...@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-boun...@nmr.mgh.**harvard.edu<freesurfer-boun...@nmr.mgh.harvard.edu>[ >>> freesurfer-boun...@nmr.mgh.**harvard.edu<freesurfer-boun...@nmr.mgh.harvard.edu>] >>> on behalf of Bruce Fischl [fis...@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<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<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<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >> > > > ---------- Forwarded message ---------- > From: Alex Hanganu <al.hang...@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: fis...@nmr.mgh.harvard.edu > > To: horton_p...@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: fis...@nmr.mgh.harvard.edu > > > To: horton_p...@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. > > > > > > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 > athttp://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. > > > > _______________________________________________ > 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. > >
_______________________________________________ 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.
