> 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
> >
> >
> >
> >
> >
> >
> >
> >