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 <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 <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<freesurfer-requ...@nmr.mgh.harvard.edu> >> >> >> >> You can reach the person managing the list at >> >> >> freesurfer-ow...@nmr.mgh.**harvard.edu<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: >> <freesur...@nmr.mgh.harvard.**edu<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/ <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: >> "freesur...@nmr.mgh.harvard.**edu<freesurfer@nmr.mgh.harvard.edu>" >> <freesur...@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>[ >> >> >> 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> >> >> >> >> >> >> >> >> >> >> ---------- Forwarded message ---------- >> >> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> >> To: "Borzello, Mia" <mborze...@partners.org> >> >> Cc: >> "freesur...@nmr.mgh.harvard.**edu<freesurfer@nmr.mgh.harvard.edu>" >> <freesur...@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.**h**arvard.edu <http://harvard.edu>< >> freesurfer-bounces@**nmr.mgh.harvard.edu<freesurfer-boun...@nmr.mgh.harvard.edu> >> >[ >> >>>> freesurfer-boun...@nmr.mgh.**h**arvard.edu <http://harvard.edu>< >> freesurfer-bounces@**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<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<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<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> >>> >> >>> >> >>> >> >>> >> >> >> >> >> >> ---------- Forwarded message ---------- >> >> From: Alex Hanganu <al.hang...@yahoo.ca> >> >> To: FS Mailing List >> >> <freesur...@nmr.mgh.harvard.**edu<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<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<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<http://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<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<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<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<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 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.
