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
>>
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>> or, via email, send a message with subject or
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>>
>> You can reach the person managing the list at
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>>
>> 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
>>
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>>
>>
>> The information in this e-mail is intended only for
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>> 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
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>> HelpLine at
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>> in
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