Hi Colin, actually there is no hard limit for the size of your input data, except for the subcortical segmentation which behaves quite strange.
What I currently do is to run recon-all on the hires data normally conforming the data. Then I use the upsampled brainmask as a mask to skullstrip my hires data and the upsampled aseg stuff to feed the upcoming stages of the recon-all pipeline. The -fix stage takes incredibly long that is why I'm trying to find a suitable work-around here. All other stages are being run normally. Although isotropic data and the -noconform flag are mandatory. Best, Falk -------- Original-Nachricht -------- > Datum: Mon, 21 Jan 2013 19:19:25 -0500 (EST) > Von: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > An: Colin Reveley <reve...@gmail.com> > CC: Joshua Lee <jki...@ucdavis.edu>, freesurfer@nmr.mgh.harvard.edu, Nick > Schmansky <ni...@nmr.mgh.harvard.edu> > Betreff: Re: [Freesurfer] beta > Hi Colin > > yes, but we simply don't have the person power to do it at the moment. Our > FS support grant ends in a month and is not going to get renewed, so it's > going to be hard to do anytime soon. > > sorry > Bruce > > > On > Mon, 21 Jan 2013, Colin Reveley wrote: > > > do you plan to support data that is more that 256^3, ever? > > > > just, do you plan to support that > > > > On 21 January 2013 22:17, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > > no, it won't change anything on the subcortical side yet > > On Mon, 21 Jan 2013, Joshua Lee wrote: > > > > > > Thanks Bruce. That sounds great. Will subcortical > segmentations also benefit yet. I remember that you once > > told me that there were > > some problems with it. > > - > > Josh > > > > > > On Mon, Jan 21, 2013 at 12:39 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu> wrote: > > 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 <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 > > > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
