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 fischl@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 <fischl@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 <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.edu<freesurfer-bounces@nmr.mgh.harvard.edu>[ >>>> 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<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.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 >> > > > >> > > > >> > > >> > > _______________________________________________ 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 >> listFreesurfer@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
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 fischl@nmr.mgh.harvard.edu An: Colin Reveley reveley@gmail.com CC: Joshua Lee jkilee@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu, Nick Schmansky nicks@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 fischl@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 subcorticalsegmentations 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 Fischlfischl@nmr.mgh.harvard.edu wrote:
Hi Josh the way we are handling sub-mm data is to run itthrough the standard recon-all, then run a
postprocessing surface deformation on the higher res data. Our preliminaryresults are pretty encouraging on T1s, T2s and
FLAIRs. cheers Bruce On Mon, 21 Jan 2013, Joshua Lee wrote: Does this mean that using Freesurfer atsub-1mm isotropic resolutions will not be possible next
version? Josh On Sun, Jan 20, 2013 at 8:07 AM, NickSchmansky nicks@nmr.mgh.harvard.edu wrote:
Colin, It will still error if anydimension is greater than 256, which then means
the flag -cw256 must be added torecon-all. This flag chops dimensions
greater than 256 down to 256.The reason it doesnt do it automatically is
that with this chopping, its notcertain that it isnt removing into the
head, so the user needs to beaware of this, so that they can inspect
orig.mgz with freeview to makesure the head is fully visible.
Nick > Does the beta permit volumesbigger than 256^3 voxels? just asking....and
> just asking about rawdimensions 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 listsubmissions to
>>freesurfer@nmr.mgh.harvard.edu
>> >> To subscribe or unsubscribevia the World Wide Web, visit
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> or, via email, send a messagewith subject or body 'help' to
>>freesurfer-request@nmr.mgh.harvard.edu
>> >> You can reach the personmanaging the list at
>>freesurfer-owner@nmr.mgh.harvard.edu
>> >> When replying, please edityour Subject line so it is more specific
>> than "Re: Contents ofFreesurfer 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: longitudinalanalysis (Alex Hanganu)
>> >> >> ---------- Forwarded message
>> From: Nick Schmansky>> To:freesurfer@nmr.mgh.harvard.edu
>> Cc: >> Date: Fri, 18 Jan 201311:20:43 -0500
>> Subject: [Freesurfer] v5.2.0beta, round two
>> For those willing and braveenough, another beta of v5.2.0 has been
>> posted >> here for you to download andtest:
>> >>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 awaitssome critical improvements to the Tracula
>> stream, but the main recon-allstream with this beta is final. The
>> final >> release is expected the firstweek of February.
>> >> Freesurfer team >> >> >> >> >> >> ---------- Forwarded message
>> From: "Borzello, Mia">> To:"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
>> Cc: >> Date: Fri, 18 Jan 201316:25:40 +0000
>> Subject: Re: [Freesurfer] pialnot computing
>> great. is there a freesurferpage on mris_topo_fixer? I'm not sure
>> how/where to run this and Idon'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] pialnot computing
>> >> Hi Mia >> >> this is fixed in the newestversion. You can grab a new mris_topo_fixer
>> and you rerun and it should beall set. You probably should take a look
>> at the ?h.orig.nofix to makesure it's reasonable (meaning no cerebellum
>> or skull attached, and thehemispherees successfully separated)
>> >> cheers >> Bruce >> On Thu, 17 >> Jan 2013, Borzello, Mia wrote: >> >> > Okay, so it didn't completewithout error. I've attached the
>> recon-all.log. Also, I wasusing 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 therecon-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 itseems that only the lh.pial computed, but
>> not the rh.pial. What would bethe 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>> To: "Borzello, Mia">> Cc:"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
>> Date: Fri, 18 Jan 201311:28:00 -0500
>> Subject: Re: [Freesurfer] pialnot 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 freesurferpage on mris_topo_fixer? I'm not sure
>>> how/where to run this and Idon'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 1:30PM
>>> To: Borzello, Mia >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] pial notcomputing
>>> >>> Hi Mia >>> >>> this is fixed in the newest version.You can grab a new mris_topo_fixer
>>> and you rerun and it should be allset. You probably should take a look
>>> at the ?h.orig.nofix to make sure it'sreasonable (meaning no
>>> cerebellum >>> or skull attached, and thehemispherees successfully separated)
>>> >>> cheers >>> Bruce >>> On Thu, 17 >>> Jan 2013, Borzello, Mia wrote: >>> >>> Okay, so it didn't complete withouterror. I've attached the
>>>> recon-all.log. Also, I was usinganother 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, 201311:22 AM
>>>> To: Borzello, Mia >>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] pial notcomputing
>>>> >>>> Hi Mia >>>> >>>> we need to see the recon-all.log. Didit end with an error?
>>>> Bruce >>>> On Thu, 17 Jan >>>> 2013, Borzello, Mia wrote: >>>> >>>> Hi Freesurfers, >>>>> >>>>> I just ran a recon, and it seemsthat only the lh.pial computed, but
>>>>> not the rh.pial. What would be thecause of this?
>>>>> Thanks, >>>>> m >>>>> >>>>>______________________________**_________________
>>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>> >>>>> >>>>> >>>>>______________________________**_________________
>>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> >>> >>>______________________________**_________________
>>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >>> >>> >>> >> >> >> ---------- Forwarded message ---------- >> From: Alex Hanganu>> To: FS Mailing ListFreesurfer@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. Myinitial analyses were performed
>> on >> mac. Though it might seem strange, someanalyses resolved after I just
>> restarted the computer. Other ones Ianalysed 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 otherscan answer?
>> > >> > thanks >> > Bruce >> > On Fri, 18 Jan 2013, paul >> > horton wrote: >> > >> > > Hi Brian, >> > > >> > > Thanks for your reply. >> > > >> > > I am running freesurfer 4.5.0. Weare using the older version so
>> that >> the >> > > analyses performed are the sameacross 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 beingrun?
>> > > >> > > Bruce >> > > On Fri, 18 Jan 2013, paul hortonwrote:
>> > > >> > > > Hi guys, >> > > > >> > > > I am currently running alongitudinal analysis on a set of scan.
>> It >> is >> > > > currently running and so far ithas taken 5 days. It seems to be
>> taking a >> > > > large amount of time on a processcalled labelling slice. I have
>> run >> the >> > > > same analysis on other subjectswhich took about 6 hours to
>> complete. So >> > > I >> > > > was wondering if you know of anyreason why a set of scans would
>> take long >> > > er >> > > > to process than others. I havechecked 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 forthe person to whom it is
>> addressed. If >> > > you believe this e-mail was sent toyou in error and the e-mail
>> contains >> > > patient information, please contactthe Partners Compliance HelpLine
>> at >> > >http://www.partners.org/complianceline . If the e-mail was sent to
>> you in >> > > error but does not contain patientinformation, please contact the
>> sender >> > > and properly dispose of the e-mail. >> > > >> > > >> >> >>
>> Freesurfer mailing >>listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >> The information in this e-mail isintended only for the person to whom
>> it is >> addressed. If you believe this e-mailwas sent to you in error and the
>> e-mail >> contains patient information, pleasecontact the Partners Compliance
>> HelpLineathttp://www.partners.org/complianceline . If the e-mail was
>> sent to you in error >> but does not contain patientinformation, 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 isintended only for the person to whom
>> it >> is >> addressed. If you believe this e-mailwas sent to you in error and the
>> e-mail >> contains patient information, pleasecontact the Partners Compliance
>> HelpLine at >> http://www.partners.org/complianceline. If the e-mail was sent to you
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> Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you cannot make a ?h.orig surface from data >256^3
I want to do that.
On 22 January 2013 11:30, "Falk Lüsebrink" falk.luese@gmx.net wrote:
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 fischl@nmr.mgh.harvard.edu An: Colin Reveley reveley@gmail.com CC: Joshua Lee jkilee@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu,
Nick Schmansky nicks@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 fischl@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 subcorticalsegmentations 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 Fischlfischl@nmr.mgh.harvard.edu wrote:
Hi Josh the way we are handling sub-mm data is to run itthrough the standard recon-all, then run a
postprocessing surface deformation on the higher res data. Our preliminaryresults are pretty encouraging on T1s, T2s and
FLAIRs. cheers Bruce On Mon, 21 Jan 2013, Joshua Lee wrote: Does this mean that using Freesurfer atsub-1mm isotropic resolutions will not be possible next
version? Josh On Sun, Jan 20, 2013 at 8:07 AM, NickSchmansky nicks@nmr.mgh.harvard.edu wrote:
Colin, It will still error if anydimension is greater than 256, which then means
the flag -cw256 must be added torecon-all. This flag chops dimensions
greater than 256 down to 256.The reason it doesnt do it automatically is
that with this chopping, its notcertain that it isnt removing into the
head, so the user needs to beaware of this, so that they can inspect
orig.mgz with freeview to makesure the head is fully visible.
Nick > Does the beta permit volumesbigger than 256^3 voxels? just asking....and
> just asking about rawdimensions 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 listsubmissions to
>>freesurfer@nmr.mgh.harvard.edu
>> >> To subscribe or unsubscribevia the World Wide Web, visit
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> or, via email, send a messagewith subject or body 'help' to
>>freesurfer-request@nmr.mgh.harvard.edu
>> >> You can reach the personmanaging the list at
>>freesurfer-owner@nmr.mgh.harvard.edu
>> >> When replying, please edityour Subject line so it is more specific
>> than "Re: Contents ofFreesurfer 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: longitudinalanalysis (Alex Hanganu)
>> >> >> ---------- Forwarded message
>> From: Nick Schmansky>> To:freesurfer@nmr.mgh.harvard.edu
>> Cc: >> Date: Fri, 18 Jan 201311:20:43 -0500
>> Subject: [Freesurfer] v5.2.0beta, round two
>> For those willing and braveenough, another beta of v5.2.0 has been
>> posted >> here for you to download andtest:
>> >>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 awaitssome critical improvements to the Tracula
>> stream, but the main recon-allstream with this beta is final. The
>> final >> release is expected the firstweek of February.
>> >> Freesurfer team >> >> >> >> >> >> ---------- Forwarded message
>> From: "Borzello, Mia">> To:"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
>> Cc: >> Date: Fri, 18 Jan 201316:25:40 +0000
>> Subject: Re: [Freesurfer] pialnot computing
>> great. is there a freesurferpage on mris_topo_fixer? I'm not sure
>> how/where to run this and Idon'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] pialnot computing
>> >> Hi Mia >> >> this is fixed in the newestversion. You can grab a new mris_topo_fixer
>> and you rerun and it should beall set. You probably should take a look
>> at the ?h.orig.nofix to makesure it's reasonable (meaning no cerebellum
>> or skull attached, and thehemispherees successfully separated)
>> >> cheers >> Bruce >> On Thu, 17 >> Jan 2013, Borzello, Mia wrote: >> >> > Okay, so it didn't completewithout error. I've attached the
>> recon-all.log. Also, I wasusing 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 therecon-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 itseems that only the lh.pial computed, but
>> not the rh.pial. What would bethe 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>> To: "Borzello, Mia">> Cc:"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
>> Date: Fri, 18 Jan 201311:28:00 -0500
>> Subject: Re: [Freesurfer] pialnot 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 freesurferpage on mris_topo_fixer? I'm not sure
>>> how/where to run this and Idon'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 1:30PM
>>> To: Borzello, Mia >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] pial notcomputing
>>> >>> Hi Mia >>> >>> this is fixed in the newest version.You can grab a new mris_topo_fixer
>>> and you rerun and it should be allset. You probably should take a look
>>> at the ?h.orig.nofix to make sure it'sreasonable (meaning no
>>> cerebellum >>> or skull attached, and thehemispherees successfully separated)
>>> >>> cheers >>> Bruce >>> On Thu, 17 >>> Jan 2013, Borzello, Mia wrote: >>> >>> Okay, so it didn't complete withouterror. I've attached the
>>>> recon-all.log. Also, I was usinganother post op patient's MRI scans.
>>>> >>>> thanks so much, >>>> m >>>>______________________________**__________
>>>> From: >>>>freesurfer-bounces@nmr.mgh.**harvard.edu<
freesurfer-bounces@nmr.mgh.harvard.edu>[
>>>>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, 201311:22 AM
>>>> To: Borzello, Mia >>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] pial notcomputing
>>>> >>>> Hi Mia >>>> >>>> we need to see the recon-all.log. Didit end with an error?
>>>> Bruce >>>> On Thu, 17 Jan >>>> 2013, Borzello, Mia wrote: >>>> >>>> Hi Freesurfers, >>>>> >>>>> I just ran a recon, and it seemsthat only the lh.pial computed, but
>>>>> not the rh.pial. What would be thecause 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%3E
>>>>> >>>>> >>>>> >>>>>______________________________**_________________
>>>> 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%3E
>>>> >>> >>>______________________________**_________________
>>> 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%3E
>>> >>> >>> >>> >> >> >> ---------- Forwarded message ---------- >> From: Alex Hanganu>> To: FS Mailing ListFreesurfer@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. Myinitial analyses were performed
>> on >> mac. Though it might seem strange, someanalyses resolved after I just
>> restarted the computer. Other ones Ianalysed 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 otherscan answer?
>> > >> > thanks >> > Bruce >> > On Fri, 18 Jan 2013, paul >> > horton wrote: >> > >> > > Hi Brian, >> > > >> > > Thanks for your reply. >> > > >> > > I am running freesurfer 4.5.0. Weare using the older version so
>> that >> the >> > > analyses performed are the sameacross 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 beingrun?
>> > > >> > > Bruce >> > > On Fri, 18 Jan 2013, paul hortonwrote:
>> > > >> > > > Hi guys, >> > > > >> > > > I am currently running alongitudinal analysis on a set of scan.
>> It >> is >> > > > currently running and so far ithas taken 5 days. It seems to be
>> taking a >> > > > large amount of time on a processcalled labelling slice. I have
>> run >> the >> > > > same analysis on other subjectswhich took about 6 hours to
>> complete. So >> > > I >> > > > was wondering if you know of anyreason why a set of scans would
>> take long >> > > er >> > > > to process than others. I havechecked 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 forthe person to whom it is
>> addressed. If >> > > you believe this e-mail was sent toyou in error and the e-mail
>> contains >> > > patient information, please contactthe Partners Compliance HelpLine
>> at >> > >http://www.partners.org/complianceline . If the e-mail was sent to
>> you in >> > > error but does not contain patientinformation, please contact the
>> sender >> > > and properly dispose of the e-mail. >> > > >> > > >> >> >>
>> Freesurfer mailing >>listFreesurfer@nmr.mgh.harvard.eduhttps://
mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >> The information in this e-mail isintended only for the person to whom
>> it is >> addressed. If you believe this e-mailwas sent to you in error and the
>> e-mail >> contains patient information, pleasecontact the Partners Compliance
>> HelpLineathttp://www.partners.org/complianceline . If the e-mail was
>> sent to you in error >> but does not contain patientinformation, 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 isintended only for the person to whom
>> it >> is >> addressed. If you believe this e-mailwas sent to you in error and the
>> e-mail >> contains patient information, pleasecontact the Partners Compliance
>> HelpLine at >> http://www.partners.org/complianceline. If the e-mail was sent to you
>> in >> error >> but does not contain patientinformation, 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.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
"Falk Lüsebrink" -
Bruce Fischl -
Colin Reveley