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.
>>
>>
> _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu
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