yes the filled.mgz is fine...with the hemispheres distinctly labelled and no cerebellum.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
and does the filled.mgz look correct? Are the hemisphere separately labeled and the cerebellum gone? Also, please post these to the list so other people can answer!
Bruce
On Thu, 22 Jun 2006, Chacko Cherian wrote:
Yes when I load the image in tkmedit I odnt have
any
problems.Its perfectly clear and
coronal,horizonatal
and sagittal are all correct.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
when you load it in tkmedit does it display properly? That is, is the coronal view really coronal? On Thu, 22 Jun 2006, Chacko Cherian wrote:
Hello all, I ran an Analyze format image in
Fresurfer...just
the
Morphometry and reconstruction tutorial..but
found
that it's creating a filled.mgz volume but I'm
having
a problem in tesselating and creating the
outputs
lh.orig and rh.orig for the left and right hemispheres.It displays a very tiny piece of the volume. Could you please let me know how to troubleshoot
this
problem.. THanks in advance.
Chacko.
Chacko Cherian M.S EE Graduate Assistant Department of Psychology Arizona State University. Tempe,AZ.
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protection around
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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can you send us the recon-all.log file? On Thu, 22 Jun 2006, Chacko Cherian wrote:
yes the filled.mgz is fine...with the hemispheres distinctly labelled and no cerebellum.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
and does the filled.mgz look correct? Are the hemisphere separately labeled and the cerebellum gone? Also, please post these to the list so other people can answer!
Bruce
On Thu, 22 Jun 2006, Chacko Cherian wrote:
Yes when I load the image in tkmedit I odnt have
any
problems.Its perfectly clear and
coronal,horizonatal
and sagittal are all correct.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
when you load it in tkmedit does it display properly? That is, is the coronal view really coronal? On Thu, 22 Jun 2006, Chacko Cherian wrote:
Hello all, I ran an Analyze format image in
Fresurfer...just
the
Morphometry and reconstruction tutorial..but
found
that it's creating a filled.mgz volume but I'm
having
a problem in tesselating and creating the
outputs
lh.orig and rh.orig for the left and right hemispheres.It displays a very tiny piece of the volume. Could you please let me know how to troubleshoot
this
problem.. THanks in advance.
Chacko.
Chacko Cherian M.S EE Graduate Assistant Department of Psychology Arizona State University. Tempe,AZ.
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam
protection around
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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--- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the recon-all.log file? On Thu, 22 Jun 2006, Chacko Cherian wrote:
yes the filled.mgz is fine...with the hemispheres distinctly labelled and no cerebellum.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
and does the filled.mgz look correct? Are the hemisphere separately labeled and the cerebellum gone? Also, please
post
these to the list so other people can answer!
Bruce
On Thu, 22 Jun 2006, Chacko Cherian wrote:
Yes when I load the image in tkmedit I odnt have
any
problems.Its perfectly clear and
coronal,horizonatal
and sagittal are all correct.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
when you load it in tkmedit does it display properly? That is, is the coronal view really coronal? On Thu, 22 Jun 2006, Chacko Cherian wrote:
Hello all, I ran an Analyze format image in
Fresurfer...just
the
Morphometry and reconstruction tutorial..but
found
that it's creating a filled.mgz volume but I'm
having
a problem in tesselating and creating the
outputs
lh.orig and rh.orig for the left and right hemispheres.It displays a very tiny piece of
the
volume. Could you please let me know how to
troubleshoot
this
problem.. THanks in advance.
Chacko.
Chacko Cherian M.S EE Graduate Assistant Department of Psychology Arizona State University. Tempe,AZ.
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam
protection around
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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hmmm, looks okay. Can you see the ?h.orig.nofix surfaces okay? On Thu, 22 Jun 2006, Chacko Cherian wrote:
--- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the recon-all.log file? On Thu, 22 Jun 2006, Chacko Cherian wrote:
yes the filled.mgz is fine...with the hemispheres distinctly labelled and no cerebellum.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
and does the filled.mgz look correct? Are the hemisphere separately labeled and the cerebellum gone? Also, please
post
these to the list so other people can answer!
Bruce
On Thu, 22 Jun 2006, Chacko Cherian wrote:
Yes when I load the image in tkmedit I odnt have
any
problems.Its perfectly clear and
coronal,horizonatal
and sagittal are all correct.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
when you load it in tkmedit does it display properly? That is, is the coronal view really coronal? On Thu, 22 Jun 2006, Chacko Cherian wrote:
> Hello all, > I ran an Analyze format image in
Fresurfer...just
the > Morphometry and reconstruction tutorial..but
found
> that it's creating a filled.mgz volume but I'm having > a problem in tesselating and creating the
outputs
> lh.orig and rh.orig for the left and right > hemispheres.It displays a very tiny piece of
the
> volume. > Could you please let me know how to
troubleshoot
this > problem.. > THanks in advance. > > Chacko. > > > > Chacko Cherian > M.S EE > Graduate Assistant > Department of Psychology > Arizona State University. > Tempe,AZ. > > >
> Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com >
> Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
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No, the nofix surfaces are also displaying just a small piece of the surface..similar to the ?h.orig surfaces.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmmm, looks okay. Can you see the ?h.orig.nofix surfaces okay? On Thu, 22 Jun 2006, Chacko Cherian wrote:
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
can you send us the recon-all.log file? On Thu, 22 Jun 2006, Chacko Cherian wrote:
yes the filled.mgz is fine...with the
hemispheres
distinctly labelled and no cerebellum.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
and does the filled.mgz look correct? Are the hemisphere separately labeled and the cerebellum gone? Also, please
post
these to the list so other people can answer!
Bruce
On Thu, 22 Jun 2006, Chacko Cherian wrote:
Yes when I load the image in tkmedit I odnt
have
any
problems.Its perfectly clear and
coronal,horizonatal
and sagittal are all correct.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
> when you load it in tkmedit does it display > properly? That is, is the > coronal view really coronal? > On Thu, 22 Jun 2006, Chacko Cherian wrote: > >> Hello all, >> I ran an Analyze format image in
Fresurfer...just
> the >> Morphometry and reconstruction tutorial..but
found
>> that it's creating a filled.mgz volume but
I'm
> having >> a problem in tesselating and creating the
outputs
>> lh.orig and rh.orig for the left and right >> hemispheres.It displays a very tiny piece of
the
>> volume. >> Could you please let me know how to
troubleshoot
> this >> problem.. >> THanks in advance. >> >> Chacko. >> >> >> >> Chacko Cherian >> M.S EE >> Graduate Assistant >> Department of Psychology >> Arizona State University. >> Tempe,AZ. >> >> >>
>> Do You Yahoo!? >> Tired of spam? Yahoo! Mail has the best
spam
> protection around >> http://mail.yahoo.com >>
>> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >> >
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Chacko,
What freesurfer distribution is being used and what platform is it installed upon?
In tksurfer, does the sample subject named 'bert' display correctly?
I guess I don't know what you mean by not tesselating correctly and not displaying the volume correctly. What tool is being used to display lh.orig or rh.orig? tksurfer? or are you refering to the surface outlines as shown in tkmedit?
Nick
No, the nofix surfaces are also displaying just a small piece of the surface..similar to the ?h.orig surfaces.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmmm, looks okay. Can you see the ?h.orig.nofix surfaces okay? On Thu, 22 Jun 2006, Chacko Cherian wrote:
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
can you send us the recon-all.log file? On Thu, 22 Jun 2006, Chacko Cherian wrote:
yes the filled.mgz is fine...with the
hemispheres
distinctly labelled and no cerebellum.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
and does the filled.mgz look correct? Are the hemisphere separately labeled and the cerebellum gone? Also, please
post
these to the list so other people can answer!
Bruce
On Thu, 22 Jun 2006, Chacko Cherian wrote:
> Yes when I load the image in tkmedit I odnt
have
any > problems.Its perfectly clear and coronal,horizonatal > and sagittal are all correct. > > --- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > >> when you load it in tkmedit does it display >> properly? That is, is the >> coronal view really coronal? >> On Thu, 22 Jun 2006, Chacko Cherian wrote: >> >>> Hello all, >>> I ran an Analyze format image in Fresurfer...just >> the >>> Morphometry and reconstruction tutorial..but found >>> that it's creating a filled.mgz volume but
I'm
>> having >>> a problem in tesselating and creating the outputs >>> lh.orig and rh.orig for the left and right >>> hemispheres.It displays a very tiny piece of
the
>>> volume. >>> Could you please let me know how to
troubleshoot
>> this >>> problem.. >>> THanks in advance. >>> >>> Chacko. >>> >>> >>> >>> Chacko Cherian >>> M.S EE >>> Graduate Assistant >>> Department of Psychology >>> Arizona State University. >>> Tempe,AZ. >>> >>> >>>
>>> Do You Yahoo!? >>> Tired of spam? Yahoo! Mail has the best
spam
>> protection around >>> http://mail.yahoo.com >>>
>>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >>> >>> >> > > >
> Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > >
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam
protection around
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick, Im just running one sample of an Analyze format image..freesurfer is installed on a Linux OS Centos4 platform..but its a 32-bit machine. the sample bert is displayed correctly... im using tksurfer to display lh.orig and rh.orig.. Nick,could this be the problem..im using a 32-bit machine but i ve downloaded the freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz version..
Regards
Chacko. --- Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Chacko,
What freesurfer distribution is being used and what platform is it installed upon?
In tksurfer, does the sample subject named 'bert' display correctly?
I guess I don't know what you mean by not tesselating correctly and not displaying the volume correctly. What tool is being used to display lh.orig or rh.orig? tksurfer? or are you refering to the surface outlines as shown in tkmedit?
Nick
No, the nofix surfaces are also displaying just a small piece of the surface..similar to the ?h.orig surfaces.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
hmmm, looks okay. Can you see the ?h.orig.nofix surfaces okay? On Thu, 22 Jun 2006, Chacko Cherian wrote:
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
can you send us the recon-all.log file? On Thu, 22 Jun 2006, Chacko Cherian wrote:
yes the filled.mgz is fine...with the
hemispheres
distinctly labelled and no cerebellum.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
> and does the filled.mgz look correct? Are
the
> hemisphere separately > labeled and the cerebellum gone? Also,
please
post
> these to the list so > other people can answer! > > Bruce > > > On Thu, 22 Jun 2006, Chacko Cherian wrote: > >> Yes when I load the image in tkmedit I odnt
have
> any >> problems.Its perfectly clear and > coronal,horizonatal >> and sagittal are all correct. >> >> --- Bruce Fischl
> wrote: >> >>> when you load it in tkmedit does it
display
>>> properly? That is, is the >>> coronal view really coronal? >>> On Thu, 22 Jun 2006, Chacko Cherian wrote: >>> >>>> Hello all, >>>> I ran an Analyze format image in > Fresurfer...just >>> the >>>> Morphometry and reconstruction
tutorial..but
> found >>>> that it's creating a filled.mgz volume
but
I'm
>>> having >>>> a problem in tesselating and creating the > outputs >>>> lh.orig and rh.orig for the left and
right
>>>> hemispheres.It displays a very tiny piece
of
the
>>>> volume. >>>> Could you please let me know how to
troubleshoot
>>> this >>>> problem.. >>>> THanks in advance. >>>> >>>> Chacko. >>>> >>>> >>>> >>>> Chacko Cherian >>>> M.S EE >>>> Graduate Assistant >>>> Department of Psychology >>>> Arizona State University. >>>> Tempe,AZ. >>>> >>>> >>>> >
>>>> Do You Yahoo!? >>>> Tired of spam? Yahoo! Mail has the best
spam
>>> protection around >>>> http://mail.yahoo.com >>>>
>>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> >>> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> >>>> >>>> >>> >> >> >>
>> Do You Yahoo!? >> Tired of spam? Yahoo! Mail has the best
spam
> protection around >> http://mail.yahoo.com >> >> >> >
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam
protection around
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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=== message truncated ===
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Chacko,
The 64bit build of freesurfer will not run on a 32bit machine. Do you have an older version of freesurfer that might be running? What is the output of:
cat $FREESURFER_HOME/build-stamp.txt
Are you sure your machine is really 32bits? Run 'uname -m' and if the machine is 64bits, it will say x86_64.
Nick
Nick, Im just running one sample of an Analyze format image..freesurfer is installed on a Linux OS Centos4 platform..but its a 32-bit machine. the sample bert is displayed correctly... im using tksurfer to display lh.orig and rh.orig.. Nick,could this be the problem..im using a 32-bit machine but i ve downloaded the freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz version..
Regards
Chacko. --- Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Chacko,
What freesurfer distribution is being used and what platform is it installed upon?
In tksurfer, does the sample subject named 'bert' display correctly?
I guess I don't know what you mean by not tesselating correctly and not displaying the volume correctly. What tool is being used to display lh.orig or rh.orig? tksurfer? or are you refering to the surface outlines as shown in tkmedit?
Nick
No, the nofix surfaces are also displaying just a small piece of the surface..similar to the ?h.orig surfaces.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
hmmm, looks okay. Can you see the ?h.orig.nofix surfaces okay? On Thu, 22 Jun 2006, Chacko Cherian wrote:
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
can you send us the recon-all.log file? On Thu, 22 Jun 2006, Chacko Cherian wrote:
> yes the filled.mgz is fine...with the
hemispheres
> distinctly labelled and no cerebellum. > > --- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > >> and does the filled.mgz look correct? Are
the
>> hemisphere separately >> labeled and the cerebellum gone? Also,
please
post >> these to the list so >> other people can answer! >> >> Bruce >> >> >> On Thu, 22 Jun 2006, Chacko Cherian wrote: >> >>> Yes when I load the image in tkmedit I odnt
have
>> any >>> problems.Its perfectly clear and >> coronal,horizonatal >>> and sagittal are all correct. >>> >>> --- Bruce Fischl
>> wrote: >>> >>>> when you load it in tkmedit does it
display
>>>> properly? That is, is the >>>> coronal view really coronal? >>>> On Thu, 22 Jun 2006, Chacko Cherian wrote: >>>> >>>>> Hello all, >>>>> I ran an Analyze format image in >> Fresurfer...just >>>> the >>>>> Morphometry and reconstruction
tutorial..but
>> found >>>>> that it's creating a filled.mgz volume
but
I'm
>>>> having >>>>> a problem in tesselating and creating the >> outputs >>>>> lh.orig and rh.orig for the left and
right
>>>>> hemispheres.It displays a very tiny piece
of
the >>>>> volume. >>>>> Could you please let me know how to troubleshoot >>>> this >>>>> problem.. >>>>> THanks in advance. >>>>> >>>>> Chacko. >>>>> >>>>> >>>>> >>>>> Chacko Cherian >>>>> M.S EE >>>>> Graduate Assistant >>>>> Department of Psychology >>>>> Arizona State University. >>>>> Tempe,AZ. >>>>> >>>>> >>>>> >>
>>>>> Do You Yahoo!? >>>>> Tired of spam? Yahoo! Mail has the best
spam
>>>> protection around >>>>> http://mail.yahoo.com >>>>>
>>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> >>>> >>> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>> >>>>> >>>>> >>>> >>> >>> >>>
>>> Do You Yahoo!? >>> Tired of spam? Yahoo! Mail has the best
spam
>> protection around >>> http://mail.yahoo.com >>> >>> >>> >> > > >
> Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam
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Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam
protection around
http://mail.yahoo.com _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
=== message truncated ===
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Nick, After running uname -m it says i686.Bit if it's a 64-bit build of freesurfer how come it ran all the other steps on my 32-bit machine?
Chacko.
--- Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Chacko,
The 64bit build of freesurfer will not run on a 32bit machine. Do you have an older version of freesurfer that might be running? What is the output of:
cat $FREESURFER_HOME/build-stamp.txt
Are you sure your machine is really 32bits? Run 'uname -m' and if the machine is 64bits, it will say x86_64.
Nick
Nick, Im just running one sample of an Analyze format image..freesurfer is installed on a Linux OS
Centos4
platform..but its a 32-bit machine. the sample bert is displayed correctly... im using tksurfer to display lh.orig and rh.orig.. Nick,could this be the problem..im using a 32-bit machine but i ve downloaded the
freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz
version..
Regards
Chacko. --- Nick Schmansky nicks@nmr.mgh.harvard.edu
wrote:
Chacko,
What freesurfer distribution is being used and
what
platform is it installed upon?
In tksurfer, does the sample subject named 'bert' display correctly?
I guess I don't know what you mean by not tesselating correctly and not displaying the volume correctly. What tool is
being
used to display lh.orig or rh.orig? tksurfer? or are you
refering
to the surface outlines as shown in tkmedit?
Nick
No, the nofix surfaces are also displaying just
a
small piece of the surface..similar to the
?h.orig
surfaces.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
hmmm, looks okay. Can you see the
?h.orig.nofix
surfaces okay? On Thu, 22 Jun 2006, Chacko Cherian wrote:
--- Bruce Fischl
wrote:
> can you send us the recon-all.log file? > On Thu, 22 Jun 2006, Chacko Cherian > wrote: > >> yes the filled.mgz is fine...with the
hemispheres
>> distinctly labelled and no cerebellum. >> >> --- Bruce Fischl
> wrote: >> >>> and does the filled.mgz look correct? Are
the
>>> hemisphere separately >>> labeled and the cerebellum gone? Also,
please
> post >>> these to the list so >>> other people can answer! >>> >>> Bruce >>> >>> >>> On Thu, 22 Jun 2006, Chacko Cherian
wrote:
>>> >>>> Yes when I load the image in tkmedit I
odnt
have
>>> any >>>> problems.Its perfectly clear and >>> coronal,horizonatal >>>> and sagittal are all correct. >>>> >>>> --- Bruce Fischl
>>> wrote: >>>> >>>>> when you load it in tkmedit does it
display
>>>>> properly? That is, is the >>>>> coronal view really coronal? >>>>> On Thu, 22 Jun 2006, Chacko Cherian
wrote:
>>>>> >>>>>> Hello all, >>>>>> I ran an Analyze format image in >>> Fresurfer...just >>>>> the >>>>>> Morphometry and reconstruction
tutorial..but
>>> found >>>>>> that it's creating a filled.mgz volume
but
I'm
>>>>> having >>>>>> a problem in tesselating and creating
the
>>> outputs >>>>>> lh.orig and rh.orig for the left and
right
>>>>>> hemispheres.It displays a very tiny
piece
of
> the >>>>>> volume. >>>>>> Could you please let me know how to > troubleshoot >>>>> this >>>>>> problem.. >>>>>> THanks in advance. >>>>>> >>>>>> Chacko. >>>>>> >>>>>> >>>>>> >>>>>> Chacko Cherian >>>>>> M.S EE >>>>>> Graduate Assistant >>>>>> Department of Psychology >>>>>> Arizona State University. >>>>>> Tempe,AZ. >>>>>> >>>>>> >>>>>> >>> >
>>>>>> Do You Yahoo!? >>>>>> Tired of spam? Yahoo! Mail has the
best
spam
>>>>> protection around >>>>>> http://mail.yahoo.com >>>>>> >
>>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> >>>>> >>>> >>> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>>> >
=== message truncated ===
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Chacko,
I'm not sure why it ran. Can you send a snapshot of the image not being displayed correctly?
When I have seen partial displays in tksurfer in the past, the problem was solved by updating the NVidia graphics driver (assuming the machine had such a card), but if subject bert is displaying correctly, then maybe the problem is with the data somehow. You could re-run subject bert if you wanted to confirm that its not a system problem.
Nick
Nick, After running uname -m it says i686.Bit if it's a 64-bit build of freesurfer how come it ran all the other steps on my 32-bit machine?
Chacko.
--- Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Chacko,
The 64bit build of freesurfer will not run on a 32bit machine. Do you have an older version of freesurfer that might be running? What is the output of:
cat $FREESURFER_HOME/build-stamp.txt
Are you sure your machine is really 32bits? Run 'uname -m' and if the machine is 64bits, it will say x86_64.
Nick
Nick, Im just running one sample of an Analyze format image..freesurfer is installed on a Linux OS
Centos4
platform..but its a 32-bit machine. the sample bert is displayed correctly... im using tksurfer to display lh.orig and rh.orig.. Nick,could this be the problem..im using a 32-bit machine but i ve downloaded the
freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz
version..
Regards
Chacko. --- Nick Schmansky nicks@nmr.mgh.harvard.edu
wrote:
Chacko,
What freesurfer distribution is being used and
what
platform is it installed upon?
In tksurfer, does the sample subject named 'bert' display correctly?
I guess I don't know what you mean by not tesselating correctly and not displaying the volume correctly. What tool is
being
used to display lh.orig or rh.orig? tksurfer? or are you
refering
to the surface outlines as shown in tkmedit?
Nick
No, the nofix surfaces are also displaying just
a
small piece of the surface..similar to the
?h.orig
surfaces.
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
hmmm, looks okay. Can you see the
?h.orig.nofix
surfaces okay? On Thu, 22 Jun 2006, Chacko Cherian wrote:
> --- Bruce Fischl
wrote: > >> can you send us the recon-all.log file? >> On Thu, 22 Jun 2006, Chacko Cherian >> wrote: >> >>> yes the filled.mgz is fine...with the hemispheres >>> distinctly labelled and no cerebellum. >>> >>> --- Bruce Fischl
>> wrote: >>> >>>> and does the filled.mgz look correct? Are
the
>>>> hemisphere separately >>>> labeled and the cerebellum gone? Also,
please
>> post >>>> these to the list so >>>> other people can answer! >>>> >>>> Bruce >>>> >>>> >>>> On Thu, 22 Jun 2006, Chacko Cherian
wrote:
>>>> >>>>> Yes when I load the image in tkmedit I
odnt
have >>>> any >>>>> problems.Its perfectly clear and >>>> coronal,horizonatal >>>>> and sagittal are all correct. >>>>> >>>>> --- Bruce Fischl
>>>> wrote: >>>>> >>>>>> when you load it in tkmedit does it
display
>>>>>> properly? That is, is the >>>>>> coronal view really coronal? >>>>>> On Thu, 22 Jun 2006, Chacko Cherian
wrote:
>>>>>> >>>>>>> Hello all, >>>>>>> I ran an Analyze format image in >>>> Fresurfer...just >>>>>> the >>>>>>> Morphometry and reconstruction
tutorial..but
>>>> found >>>>>>> that it's creating a filled.mgz volume
but
I'm >>>>>> having >>>>>>> a problem in tesselating and creating
the
>>>> outputs >>>>>>> lh.orig and rh.orig for the left and
right
>>>>>>> hemispheres.It displays a very tiny
piece
of
>> the >>>>>>> volume. >>>>>>> Could you please let me know how to >> troubleshoot >>>>>> this >>>>>>> problem.. >>>>>>> THanks in advance. >>>>>>> >>>>>>> Chacko. >>>>>>> >>>>>>> >>>>>>> >>>>>>> Chacko Cherian >>>>>>> M.S EE >>>>>>> Graduate Assistant >>>>>>> Department of Psychology >>>>>>> Arizona State University. >>>>>>> Tempe,AZ. >>>>>>> >>>>>>> >>>>>>> >>>> >>
>>>>>>> Do You Yahoo!? >>>>>>> Tired of spam? Yahoo! Mail has the
best
spam >>>>>> protection around >>>>>>> http://mail.yahoo.com >>>>>>> >>
>>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> >>>>>> >>>>> >>>> >>> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> >>
=== message truncated ===
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Nick,
Sorry for the delay.I ve attached the image which opens when I use tksurfer and run rh.pial.Bert also gave me a similar image.Please have a look at it.
THanks a lot,
Chacko Cherian
Graduate Research Assistant Department of Psychology Arizona State University. Tempe,AZ.
--- Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Chacko,
I'm not sure why it ran. Can you send a snapshot of the image not being displayed correctly?
When I have seen partial displays in tksurfer in the past, the problem was solved by updating the NVidia graphics driver (assuming the machine had such a card), but if subject bert is displaying correctly, then maybe the problem is with the data somehow. You could re-run subject bert if you wanted to confirm that its not a system problem.
Nick
Nick, After running uname -m it says i686.Bit if it's a 64-bit build of freesurfer how come it ran all the other steps on my 32-bit machine?
Chacko.
--- Nick Schmansky nicks@nmr.mgh.harvard.edu
wrote:
Chacko,
The 64bit build of freesurfer will not run on a 32bit machine. Do you have an older version of freesurfer that might be running? What is the output of:
cat $FREESURFER_HOME/build-stamp.txt
Are you sure your machine is really 32bits? Run 'uname -m' and if the machine is 64bits, it will say x86_64.
Nick
Nick, Im just running one sample of an Analyze format image..freesurfer is installed on a Linux OS
Centos4
platform..but its a 32-bit machine. the sample bert is displayed correctly... im using tksurfer to display lh.orig and
rh.orig..
Nick,could this be the problem..im using a
32-bit
machine but i ve downloaded the
freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz
version..
Regards
Chacko. --- Nick Schmansky nicks@nmr.mgh.harvard.edu
wrote:
Chacko,
What freesurfer distribution is being used and
what
platform is it installed upon?
In tksurfer, does the sample subject named
'bert'
display correctly?
I guess I don't know what you mean by not tesselating correctly and not displaying the volume correctly. What tool is
being
used to display lh.orig or rh.orig? tksurfer? or are you
refering
to the surface outlines as shown in tkmedit?
Nick
No, the nofix surfaces are also displaying
just
a
small piece of the surface..similar to the
?h.orig
surfaces.
--- Bruce Fischl
wrote:
> hmmm, looks okay. Can you see the
?h.orig.nofix
> surfaces okay? > On Thu, 22 > Jun 2006, Chacko Cherian wrote: > > > --- Bruce Fischl
> wrote: > > > >> can you send us the recon-all.log file? > >> On Thu, 22 Jun 2006, Chacko Cherian > >> wrote: > >> > >>> yes the filled.mgz is fine...with the > hemispheres > >>> distinctly labelled and no cerebellum. > >>> > >>> --- Bruce Fischl
> >> wrote: > >>> > >>>> and does the filled.mgz look correct?
Are
the
> >>>> hemisphere separately > >>>> labeled and the cerebellum gone? Also,
please
> >> post > >>>> these to the list so > >>>> other people can answer! > >>>> > >>>> Bruce > >>>> > >>>> > >>>> On Thu, 22 Jun 2006, Chacko Cherian
wrote:
> >>>> > >>>>> Yes when I load the image in tkmedit
I
odnt
> have > >>>> any > >>>>> problems.Its perfectly clear and > >>>> coronal,horizonatal > >>>>> and sagittal are all correct. > >>>>> > >>>>> --- Bruce Fischl
> >>>> wrote: > >>>>> > >>>>>> when you load it in tkmedit does it
display
> >>>>>> properly? That is, is the > >>>>>> coronal view really coronal? > >>>>>> On Thu, 22 Jun 2006, Chacko Cherian
wrote:
> >>>>>> > >>>>>>> Hello all, > >>>>>>> I ran an Analyze format image in > >>>> Fresurfer...just > >>>>>> the > >>>>>>> Morphometry and reconstruction
tutorial..but
> >>>> found > >>>>>>> that it's creating a filled.mgz
volume
but
> I'm > >>>>>> having > >>>>>>> a problem in tesselating and
creating
the
> >>>> outputs > >>>>>>> lh.orig and rh.orig for the left
and
right
> >>>>>>> hemispheres.It displays a very tiny
piece
of
> >> the > >>>>>>> volume. > >>>>>>> Could you please let me know how to > >> troubleshoot > >>>>>> this > >>>>>>> problem.. > >>>>>>> THanks in advance. > >>>>>>> > >>>>>>> Chacko. > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> Chacko Cherian > >>>>>>> M.S EE > >>>>>>> Graduate Assistant > >>>>>>> Department of Psychology > >>>>>>> Arizona State University. > >>>>>>> Tempe,AZ.
=== message truncated ===
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freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Chacko Cherian -
Nick Schmansky