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 <ni...@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-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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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