date:20070514

[Freesurfer] reg- feat2anat error

2007-05-14 Thread Furlong, Carolyn

Hi, 

When I try to register my functional data to anatomical data using 

reg-feat2anat --feat feat_directory --subject subject_name

I get the following error message 

ERROR: could not read ///example_func.nii.gz as 24

What does this mean? And how can I fix this?

Best wishes
Carolyn
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Re: [Freesurfer] Make_average_subject error

2007-05-14 Thread Furlong, Carolyn

Thanks Doug, 
 
I have tried your suggestion and set the command make_average_subject running 
again.  I has been going for several hours but there is no visible 
change/activity on the console, is this unusual?.   
 
Also, there are only 13 subjects, how long would you expect this process to 
take per subject?
 
Best wishes
Carolyn



From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Wed 5/9/2007 6:21 PM
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Make_average_subject error



you may be using a version that does not have this option. Try using these

doug

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_subject
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface

Furlong, Carolyn wrote: 


Hi all,

I tried running it again with --no-symlink but this error came up

ERROR: Flag --no-symlink unrecognized.

any advice?

Best wishes
Carolyn 





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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] Make_average_subject error

2007-05-14 Thread Doug Greve

it should not be taking that long. It must be hanging somewhere. Try 
re-running it with --debug as the first option. It will print out a 
bunch of stuff to the screen, but you should be able to see where it 
hangs (if it does).


doug

Furlong, Carolyn wrote:


Thanks Doug,
 
I have tried your suggestion and set the command make_average_subject 
running again.  I has been going for several hours but there is no 
visible change/activity on the console, is this unusual?.   
 
Also, there are only 13 subjects, how long would you expect this 
process to take per subject?
 
Best wishes

Carolyn


From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Wed 5/9/2007 6:21 PM
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Make_average_subject error


you may be using a version that does not have this option. Try using these

doug

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_subject
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface

Furlong, Carolyn wrote:



Hi all,

I tried running it again with --no-symlink but this error came up

ERROR: Flag --no-symlink unrecognized.

any advice?

Best wishes
Carolyn



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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

 




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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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[Freesurfer] (no subject)

2007-05-14 Thread hankee

hi,I have some question to ask,
   First,now I want to add four parts of the occipital lobe's gray matter 
volume(Lateral Occipital,Lingual,Cuneus,Pericalcarine) to evaluate occipital 
lobe development,can I do like this?
   second, I also want to use the occipital lobe's cortical thickness to 
evaluate development,but four parts of the occipital's cortical thickness is 
different,so I add the four parts of the cortical thickness and divide 4,after 
that I get the average value,then use this average value to do  statistics 
analysis,can I also do like this?
Thank you very much!
hankee
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[Freesurfer] question about 'mris_wm_volume: error while loading shared libraries: libstdc++.so.6'

2007-05-14 Thread Ruiwang Huang

Dear All

I meet a problem when I run the command 
  mris_wm_volume
to calculate the white matter volume for each hemisphere.

The error message is coplied here
>> mris_wm_volume
>> mris_wm_volume: error while loading shared libraries: libstdc++.so.6: 
cannot open shared object file: No such file or directory

Does any one know how to solve the problem? (My PC installed Suse9.3)

Many thanks in advance

Rhuang

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Re: [Freesurfer] question about 'mris_wm_volume: error while loading shared libraries: libstdc++.so.6'

2007-05-14 Thread Nick Schmansky

Rhuang,

I'm guessing that you're using our Centos freesurfer distribution (type:
cat $FREESURFER_HOME/build-stamp.txt   to find out).  You'll want to use
our RedHat 9 freesurfer distribution with Suse9.3.

Nick


On Mon, 2007-05-14 at 17:05 +0200, Ruiwang Huang wrote:
> Dear All
> 
> I meet a problem when I run the command 
>   mris_wm_volume
> to calculate the white matter volume for each hemisphere.
> 
> The error message is coplied here
> >> mris_wm_volume
> >> mris_wm_volume: error while loading shared libraries: libstdc++.so.6: 
> cannot open shared object file: No such file or directory
> 
> Does any one know how to solve the problem? (My PC installed Suse9.3)
> 
> Many thanks in advance
> 
> Rhuang
> 
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> 
> 

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Re: [Freesurfer] question about 'mris_wm_volume: error whileloading shared libraries: libstdc++.so.6'

2007-05-14 Thread Ruiwang Huang

Dear Nick

Many thanks for your message. 

Here is the output after my typing 
  >> cat $FREESURFER_HOME/build-stamp.txt
  >> freesurfer-Linux-rh9-stable-pub-v3.0.3

Do I need update the freesurfer on my PC?


Ruiwang

On Monday 14 May 2007 17:26, you wrote:
> Rhuang,
>
> I'm guessing that you're using our Centos freesurfer distribution (type:
> cat $FREESURFER_HOME/build-stamp.txt   to find out).  You'll want to use
> our RedHat 9 freesurfer distribution with Suse9.3.
>
> Nick
>
> On Mon, 2007-05-14 at 17:05 +0200, Ruiwang Huang wrote:
> > Dear All
> >
> > I meet a problem when I run the command
> >   mris_wm_volume
> > to calculate the white matter volume for each hemisphere.
> >
> > The error message is coplied here
> >
> > >> mris_wm_volume
> > >> mris_wm_volume: error while loading shared libraries: libstdc++.so.6:
> >
> > cannot open shared object file: No such file or directory
> >
> > Does any one know how to solve the problem? (My PC installed Suse9.3)
> >
> > Many thanks in advance
> >
> > Rhuang
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] quick scatterplot label question

2007-05-14 Thread Kevin Teich

This is the MeasurementName in the .fsgdf file.

On Sun, 2007-05-13 at 23:03 +0100, Morgan Hough wrote:
> Once I have defined a label in tksurfer and I select *Tools -> *Group* 
> -> Graph Marked Vertices Avg to open a scatterplot window, how do I 
> change the y axis label from the default "external" label. I assume that 
> I need to set this beforehand in the fsgd file but I wasn't sure how. 
> Thanks in advance.


-- 
Kevin Teich

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Re: [Freesurfer] can't load sig.mgh in dev tksurfer

2007-05-14 Thread Kevin Teich

This suggests that the number of values in the .mgh file is different
than the number of vertices in the surface. Did you regenerate the
surface after generating the .mgh file?

On Sun, 2007-05-13 at 15:29 -0400, Catherine Hartley wrote:
> Hi,
> 
> I'm having a problem with the development version of tksurfer.  When  
> I try to load a sig.mgh file as an overlay, I get the following error:
> 
> % surfer: couldn't load /Applications/freesurfer/subjects/reruns/ 
> glmleft/ReappCSplusContrast/sig.mgh
> sclv_read_from_volume: error in FunD_New
> 
> Thanks,
> Cate
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> 
-- 
Kevin Teich

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Re: [Freesurfer] can't load sig.mgh in dev tksurfer

2007-05-14 Thread Bruce Fischl

you can use mri_info on the .mgh file to check (and mris_info on the 
surface)

On Mon, 14 May 2007, Kevin Teich wrote:


This suggests that the number of values in the .mgh file is different
than the number of vertices in the surface. Did you regenerate the
surface after generating the .mgh file?

On Sun, 2007-05-13 at 15:29 -0400, Catherine Hartley wrote:

Hi,

I'm having a problem with the development version of tksurfer.  When
I try to load a sig.mgh file as an overlay, I get the following error:

% surfer: couldn't load /Applications/freesurfer/subjects/reruns/
glmleft/ReappCSplusContrast/sig.mgh
sclv_read_from_volume: error in FunD_New

Thanks,
Cate
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Re: [Freesurfer] question about 'mris_wm_volume: error whileloading shared libraries: libstdc++.so.6'

2007-05-14 Thread Nick Schmansky

Ruiwang,

It looks like you are already running what I thought would be the
correct version (rh9 is redhat 9).  Can you send me the output of this
command?

  ldd `which mris_wm_volume`

Nick


On Mon, 2007-05-14 at 17:43 +0200, Ruiwang Huang wrote:
> Dear Nick
> 
> Many thanks for your message. 
> 
> Here is the output after my typing 
>   >> cat $FREESURFER_HOME/build-stamp.txt
>   >> freesurfer-Linux-rh9-stable-pub-v3.0.3
> 
> Do I need update the freesurfer on my PC?
> 
> 
> Ruiwang
> 
> On Monday 14 May 2007 17:26, you wrote:
> > Rhuang,
> >
> > I'm guessing that you're using our Centos freesurfer distribution (type:
> > cat $FREESURFER_HOME/build-stamp.txt   to find out).  You'll want to use
> > our RedHat 9 freesurfer distribution with Suse9.3.
> >
> > Nick
> >
> > On Mon, 2007-05-14 at 17:05 +0200, Ruiwang Huang wrote:
> > > Dear All
> > >
> > > I meet a problem when I run the command
> > >   mris_wm_volume
> > > to calculate the white matter volume for each hemisphere.
> > >
> > > The error message is coplied here
> > >
> > > >> mris_wm_volume
> > > >> mris_wm_volume: error while loading shared libraries: libstdc++.so.6:
> > >
> > > cannot open shared object file: No such file or directory
> > >
> > > Does any one know how to solve the problem? (My PC installed Suse9.3)
> > >
> > > Many thanks in advance
> > >
> > > Rhuang
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 

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Re: [Freesurfer] question about 'mris_wm_volume: errorwhileloading shared libraries: libstdc++.so.6'

2007-05-14 Thread Ruiwang Huang

Dear Nick 

Thanks a lot. Here is the output of ' ldd `which mris_wm_volume`

linux-gate.so.1 =>  (0xe000)
libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x40019000)
libtiff.so.3 => /usr/lib/libtiff.so.3 (0x40038000)
libz.so.1 => /lib/libz.so.1 (0x40088000)
libcrypt.so.1 => /lib/libcrypt.so.1 (0x40099000)
libstdc++.so.6 => not found
libm.so.6 => /lib/tls/libm.so.6 (0x400eb000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x4010e000)
libc.so.6 => /lib/tls/libc.so.6 (0x40116000)
libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x4022f000)
/lib/ld-linux.so.2 (0x4000)

Any suggestions please?

Rhuang


On Monday 14 May 2007 17:53, Nick Schmansky wrote:
> Ruiwang,
>
> It looks like you are already running what I thought would be the
> correct version (rh9 is redhat 9).  Can you send me the output of this
> command?
>
>   ldd `which mris_wm_volume`
>
> Nick
>
> On Mon, 2007-05-14 at 17:43 +0200, Ruiwang Huang wrote:
> > Dear Nick
> >
> > Many thanks for your message.
> >
> > Here is the output after my typing
> >
> >   >> cat $FREESURFER_HOME/build-stamp.txt
> >   >> freesurfer-Linux-rh9-stable-pub-v3.0.3
> >
> > Do I need update the freesurfer on my PC?
> >
> >
> > Ruiwang
> >
> > On Monday 14 May 2007 17:26, you wrote:
> > > Rhuang,
> > >
> > > I'm guessing that you're using our Centos freesurfer distribution
> > > (type: cat $FREESURFER_HOME/build-stamp.txt   to find out).  You'll
> > > want to use our RedHat 9 freesurfer distribution with Suse9.3.
> > >
> > > Nick
> > >
> > > On Mon, 2007-05-14 at 17:05 +0200, Ruiwang Huang wrote:
> > > > Dear All
> > > >
> > > > I meet a problem when I run the command
> > > >   mris_wm_volume
> > > > to calculate the white matter volume for each hemisphere.
> > > >
> > > > The error message is coplied here
> > > >
> > > > >> mris_wm_volume
> > > > >> mris_wm_volume: error while loading shared libraries:
> > > > >> libstdc++.so.6:
> > > >
> > > > cannot open shared object file: No such file or directory
> > > >
> > > > Does any one know how to solve the problem? (My PC installed Suse9.3)
> > > >
> > > > Many thanks in advance
> > > >
> > > > Rhuang
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
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Re: [Freesurfer] question about 'mris_wm_volume: errorwhileloading shared libraries: libstdc++.so.6'

2007-05-14 Thread Nick Schmansky

Rhuang,

I just realized that mris_wm_volume is not part of the stable release,
so you must have gotten the 'dev' release of it at some point in time,
and probably got the Centos build of mris_wm_volume (which uses libstdc+
+.so.6).

So I have posted the 'rh9' build of mris_wm_volume here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/linux

Be sure to 'chmod a+x mris_wm_volume' after you copy it to your
$FREESURFER_HOME/bin.

Nick


On Mon, 2007-05-14 at 18:14 +0200, Ruiwang Huang wrote: 
> Dear Nick 
> 
> Thanks a lot. Here is the output of ' ldd `which mris_wm_volume`
> 
> linux-gate.so.1 =>  (0xe000)
> libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x40019000)
> libtiff.so.3 => /usr/lib/libtiff.so.3 (0x40038000)
> libz.so.1 => /lib/libz.so.1 (0x40088000)
> libcrypt.so.1 => /lib/libcrypt.so.1 (0x40099000)
> libstdc++.so.6 => not found
> libm.so.6 => /lib/tls/libm.so.6 (0x400eb000)
> libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x4010e000)
> libc.so.6 => /lib/tls/libc.so.6 (0x40116000)
> libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x4022f000)
> /lib/ld-linux.so.2 (0x4000)
> 
> Any suggestions please?
> 
> Rhuang
> 
> 
> On Monday 14 May 2007 17:53, Nick Schmansky wrote:
> > Ruiwang,
> >
> > It looks like you are already running what I thought would be the
> > correct version (rh9 is redhat 9).  Can you send me the output of this
> > command?
> >
> >   ldd `which mris_wm_volume`
> >
> > Nick
> >
> > On Mon, 2007-05-14 at 17:43 +0200, Ruiwang Huang wrote:
> > > Dear Nick
> > >
> > > Many thanks for your message.
> > >
> > > Here is the output after my typing
> > >
> > >   >> cat $FREESURFER_HOME/build-stamp.txt
> > >   >> freesurfer-Linux-rh9-stable-pub-v3.0.3
> > >
> > > Do I need update the freesurfer on my PC?
> > >
> > >
> > > Ruiwang
> > >
> > > On Monday 14 May 2007 17:26, you wrote:
> > > > Rhuang,
> > > >
> > > > I'm guessing that you're using our Centos freesurfer distribution
> > > > (type: cat $FREESURFER_HOME/build-stamp.txt   to find out).  You'll
> > > > want to use our RedHat 9 freesurfer distribution with Suse9.3.
> > > >
> > > > Nick
> > > >
> > > > On Mon, 2007-05-14 at 17:05 +0200, Ruiwang Huang wrote:
> > > > > Dear All
> > > > >
> > > > > I meet a problem when I run the command
> > > > >   mris_wm_volume
> > > > > to calculate the white matter volume for each hemisphere.
> > > > >
> > > > > The error message is coplied here
> > > > >
> > > > > >> mris_wm_volume
> > > > > >> mris_wm_volume: error while loading shared libraries:
> > > > > >> libstdc++.so.6:
> > > > >
> > > > > cannot open shared object file: No such file or directory
> > > > >
> > > > > Does any one know how to solve the problem? (My PC installed Suse9.3)
> > > > >
> > > > > Many thanks in advance
> > > > >
> > > > > Rhuang
> > > > >
> > > > > ___
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 

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Re: [Freesurfer] question about 'mris_wm_volume: errorwhileloading shared libraries: libstdc++.so.6'

2007-05-14 Thread Ruiwang Huang

Dear Nick 

Thanks a lot. Here is the output of ' ldd `which mris_wm_volume`

linux-gate.so.1 =>  (0xe000)
libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x40019000)
libtiff.so.3 => /usr/lib/libtiff.so.3 (0x40038000)
libz.so.1 => /lib/libz.so.1 (0x40088000)
libcrypt.so.1 => /lib/libcrypt.so.1 (0x40099000)
libstdc++.so.6 => not found
libm.so.6 => /lib/tls/libm.so.6 (0x400eb000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x4010e000)
libc.so.6 => /lib/tls/libc.so.6 (0x40116000)
libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x4022f000)
/lib/ld-linux.so.2 (0x4000)

Any suggestions please?

Rhuang


On Monday 14 May 2007 17:53, Nick Schmansky wrote:
> Ruiwang,
>
> It looks like you are already running what I thought would be the
> correct version (rh9 is redhat 9).  Can you send me the output of this
> command?
>
>   ldd `which mris_wm_volume`
>
> Nick
>
> On Mon, 2007-05-14 at 17:43 +0200, Ruiwang Huang wrote:
> > Dear Nick
> >
> > Many thanks for your message.
> >
> > Here is the output after my typing
> >
> >   >> cat $FREESURFER_HOME/build-stamp.txt
> >   >> freesurfer-Linux-rh9-stable-pub-v3.0.3
> >
> > Do I need update the freesurfer on my PC?
> >
> >
> > Ruiwang
> >
> > On Monday 14 May 2007 17:26, you wrote:
> > > Rhuang,
> > >
> > > I'm guessing that you're using our Centos freesurfer distribution
> > > (type: cat $FREESURFER_HOME/build-stamp.txt   to find out).  You'll
> > > want to use our RedHat 9 freesurfer distribution with Suse9.3.
> > >
> > > Nick
> > >
> > > On Mon, 2007-05-14 at 17:05 +0200, Ruiwang Huang wrote:
> > > > Dear All
> > > >
> > > > I meet a problem when I run the command
> > > >   mris_wm_volume
> > > > to calculate the white matter volume for each hemisphere.
> > > >
> > > > The error message is coplied here
> > > >
> > > > >> mris_wm_volume
> > > > >> mris_wm_volume: error while loading shared libraries:
> > > > >> libstdc++.so.6:
> > > >
> > > > cannot open shared object file: No such file or directory
> > > >
> > > > Does any one know how to solve the problem? (My PC installed Suse9.3)
> > > >
> > > > Many thanks in advance
> > > >
> > > > Rhuang
> > > >
> > > > ___
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Re: [Freesurfer] reg- feat2anat error

2007-05-14 Thread Doug Greve


can you send the log file?

Furlong, Carolyn wrote:


Hi,

When I try to register my functional data to anatomical data using

reg-feat2anat --feat feat_directory --subject subject_name

I get the following error message

ERROR: could not read ///example_func.nii.gz as 24

What does this mean? And how can I fix this?

Best wishes
Carolyn



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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] question about 'mris_wm_volume: errorwhileloadingshared libraries: libstdc++.so.6'

2007-05-14 Thread Ruiwang Huang

Dear Nick

Thanks a lot. It works.

Have a very nice day

Rhuang

On Monday 14 May 2007 18:23, you wrote:
> Rhuang,
>
> I just realized that mris_wm_volume is not part of the stable release,
> so you must have gotten the 'dev' release of it at some point in time,
> and probably got the Centos build of mris_wm_volume (which uses libstdc+
> +.so.6).
>
> So I have posted the 'rh9' build of mris_wm_volume here:
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/linux
>
> Be sure to 'chmod a+x mris_wm_volume' after you copy it to your
> $FREESURFER_HOME/bin.
>
> Nick
>
> On Mon, 2007-05-14 at 18:14 +0200, Ruiwang Huang wrote:
> > Dear Nick
> >
> > Thanks a lot. Here is the output of ' ldd `which mris_wm_volume`
> >
> > linux-gate.so.1 =>  (0xe000)
> > libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x40019000)
> > libtiff.so.3 => /usr/lib/libtiff.so.3 (0x40038000)
> > libz.so.1 => /lib/libz.so.1 (0x40088000)
> > libcrypt.so.1 => /lib/libcrypt.so.1 (0x40099000)
> > libstdc++.so.6 => not found
> > libm.so.6 => /lib/tls/libm.so.6 (0x400eb000)
> > libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x4010e000)
> > libc.so.6 => /lib/tls/libc.so.6 (0x40116000)
> > libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x4022f000)
> > /lib/ld-linux.so.2 (0x4000)
> >
> > Any suggestions please?
> >
> > Rhuang
> >
> > On Monday 14 May 2007 17:53, Nick Schmansky wrote:
> > > Ruiwang,
> > >
> > > It looks like you are already running what I thought would be the
> > > correct version (rh9 is redhat 9).  Can you send me the output of this
> > > command?
> > >
> > >   ldd `which mris_wm_volume`
> > >
> > > Nick
> > >
> > > On Mon, 2007-05-14 at 17:43 +0200, Ruiwang Huang wrote:
> > > > Dear Nick
> > > >
> > > > Many thanks for your message.
> > > >
> > > > Here is the output after my typing
> > > >
> > > >   >> cat $FREESURFER_HOME/build-stamp.txt
> > > >   >> freesurfer-Linux-rh9-stable-pub-v3.0.3
> > > >
> > > > Do I need update the freesurfer on my PC?
> > > >
> > > >
> > > > Ruiwang
> > > >
> > > > On Monday 14 May 2007 17:26, you wrote:
> > > > > Rhuang,
> > > > >
> > > > > I'm guessing that you're using our Centos freesurfer distribution
> > > > > (type: cat $FREESURFER_HOME/build-stamp.txt   to find out).  You'll
> > > > > want to use our RedHat 9 freesurfer distribution with Suse9.3.
> > > > >
> > > > > Nick
> > > > >
> > > > > On Mon, 2007-05-14 at 17:05 +0200, Ruiwang Huang wrote:
> > > > > > Dear All
> > > > > >
> > > > > > I meet a problem when I run the command
> > > > > >   mris_wm_volume
> > > > > > to calculate the white matter volume for each hemisphere.
> > > > > >
> > > > > > The error message is coplied here
> > > > > >
> > > > > > >> mris_wm_volume
> > > > > > >> mris_wm_volume: error while loading shared libraries:
> > > > > > >> libstdc++.so.6:
> > > > > >
> > > > > > cannot open shared object file: No such file or directory
> > > > > >
> > > > > > Does any one know how to solve the problem? (My PC installed
> > > > > > Suse9.3)
> > > > > >
> > > > > > Many thanks in advance
> > > > > >
> > > > > > Rhuang
> > > > > >
> > > > > > ___
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> > >
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[Freesurfer] surf-sess error

2007-05-14 Thread Lee, Jung Min

Hi, 
 
I was able to use surf-sess command (modified in our group) to take pictures
(rgb) of the brain; however, several days ago, I was kept getting errors (even
errors with commands that worked fine before). it keep saying tksurfer.new:
Command not found., then quit. Would you help me out?
 
Machine: Roma /space/roma/1/users/caplan/plaus2
Env: Standard environment 
Subjects_Dir: /space/thor/1/users/west/subjects
 
[roma:plaus2] (nmr-std-env)
/space/roma/1/users/caplan/plaus2/scripts/surf-sess-rgb_wfile \
? -analysis plaus2_corr \
? -space sph \
? -spacedir sph20 \
? -subject west_margaret \
? -s isxavg-plaus2_corr \
? -contrast implaus_plaus_8-12sum \
? -map sig \
? -fthresh 1.3 \
? -fmid 2.0 \
? -fslope 1 \
? -df dir \
? -isxavg random \
? -avgcurv \
? -offset 0 \
? -wfile
/space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm
in16_minarea300_lh_o.w \
? -hemi lh \
? -rgbname plaus2_corr_implaus_plaus_8-12sum_300
cat: /usr/local/freesurfer/stable/fsfast/docs/version: No such file or directory
-
surf-sess logfile is /dev/null
-
 
-->>>
INFO: You are about to use the NEW version of tksurfer.
INFO: If you want to use the OLD version, re-run surf-sess
INFO: with the -old flag.
-->>>
 
--
--
Session: isxavg-plaus2_corr 
-- lh hemisphere --
sig-0-west_margaret
west_margaret
nowsource
west_margaret
equal
wfile is
/space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm
in16_minarea300_lh_o.w
 tcl file ---
set val
/space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm
in16_minarea300_lh_o.w
sclv_read_binary_values 0
set curv lh.avg_curv
read_binary_curv;
set curvflag 1;
source /usr/local/freesurfer/stable/lib/tcl/readenv.tcl
file mkdir /autofs/space/roma_001/users/caplan/plaus2/rgb
file mkdir /autofs/space/roma_001/users/caplan/plaus2/rgb
open_window
sclv_set_current_field 0
puts "Taking Snapshots..."
make_lateral_view
redraw
set rgb
/autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum
_300_lh_lat.rgb
save_rgb
rotate_brain_x 90
redraw
set rgb
/autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum
_300_lh_ven.rgb
save_rgb
make_lateral_view
rotate_brain_y 180
redraw
set rgb
/autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum
_300_lh_med.rgb
save_rgb
exit
-
--
/autofs/space/roma_001/users/caplan/plaus2/isxavg-plaus2_corr/bold/plaus2_corr/s
ph20-rfx/implaus_plaus_8-12sum
tksurfer.new -west_margaret lh inflated -tcl /tmp/surf-sess-22861.tcl
--
tksurfer.new: Command not found.
Mon May 14 12:43:08 EDT 2007

I am also attaching the /surf-sess-rgb_wfile under command line. 
 
Thanks a lot!
-Jung Min
 
 
** 
Jung Min Lee 
Neurology/Neuropsychology 
Martinos Center for Biomedical Imaging 
Massachusetts General Hospital
Tel: 617-726-0303 (work) 
   617-780-1900 (cell) 
e-mail: [EMAIL PROTECTED]   
 [EMAIL PROTECTED]  
**
#!/bin/csh -f
# surf-sess
#
set VERSION = '$Id: surf-sess,v 1.1 2003/03/04 21:22:09 greve Exp $'
set FASTVER = `cat $FMRI_ANALYSIS_DIR/docs/version`;
set inputargs = ($argv);

set analysis = ();
set contrast = ();
set rtopymode= ();
set rtopy= 0;
set angleoffset  = ();
set angleoffsetcode = ();
set map  = sig;
set imageoffset  = 0;
set grpname  = ();
set space= native;
set spacedir = ();
set norgb= 0;
set rgbstem  = ();
set ScriptOnly   = 0;
set umaskarg = ();
set hemilist = ();
set subject  = ();
set resetsubject = 0;
set srcsubject   = ();
set smoothsteps  = ();
set surf = ();
set SessList = ();
set isxavgmethod = ();
set nolog = 0;
set nowait = 0;
set flat = 0;
set patch = ();
set UseAvgCurv = 0;
set code = (); # a way to uniquely id a paint, issued by paint-sess
set usenew = ".new";
set usertcl = ();

set Medial  = 1;
set Lateral = 1;
set Ventral = 1;

set rgbwd = `pwd`;

## tksurfer variables ###
setenv fthresh   2.0
setenv fslope0.1
setenv fmid  5.0

if($#argv == 0) then
  goto usage_exit;
  exit 1;
endif

set n = `echo $argv | grep version | wc -l` 
if($n != 0) then
  echo $VERSION
  exit 0;
endif

## Look for nolog option ##
set n = `echo $argv | grep nolog | wc -l` 
if($n != 0) then
  set nolog = 1;
endif

# Create a log file ##
if(! $nolog) then
  set logdir = `pwd`/log;
  mkdir -p $logdir

Re: [Freesurfer] can't load sig.mgh in dev tksurfer

2007-05-14 Thread Catherine Hartley


Hi,

I can't seem to get the syntax right for mri_info or mris_info to  
work, but i did not regenerate the surfaces after generating the .mgh  
file, so the number of vertices should be the same.  Any other  
possibilities?  Should I just rerun the mri_glmfit that generated the  
sig.mgh file?


-Cate

On May 14, 2007, at 11:50 AM, Bruce Fischl wrote:

you can use mri_info on the .mgh file to check (and mris_info on  
the surface)

On Mon, 14 May 2007, Kevin Teich wrote:


This suggests that the number of values in the .mgh file is different
than the number of vertices in the surface. Did you regenerate the
surface after generating the .mgh file?

On Sun, 2007-05-13 at 15:29 -0400, Catherine Hartley wrote:

Hi,

I'm having a problem with the development version of tksurfer.  When
I try to load a sig.mgh file as an overlay, I get the following  
error:


% surfer: couldn't load /Applications/freesurfer/subjects/reruns/
glmleft/ReappCSplusContrast/sig.mgh
sclv_read_from_volume: error in FunD_New

Thanks,
Cate
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Re: [Freesurfer] can't load sig.mgh in dev tksurfer

2007-05-14 Thread Bruce Fischl


Hi Cate,

there's not much syntax to get write. They take either a volume or a 
surface file, with the full path.


Bruce

On Mon, 14 May 2007, Catherine Hartley 
wrote:



Hi,

I can't seem to get the syntax right for mri_info or mris_info to work, but i 
did not regenerate the surfaces after generating the .mgh file, so the number 
of vertices should be the same.  Any other possibilities?  Should I just 
rerun the mri_glmfit that generated the sig.mgh file?


-Cate

On May 14, 2007, at 11:50 AM, Bruce Fischl wrote:

you can use mri_info on the .mgh file to check (and mris_info on the 
surface)

On Mon, 14 May 2007, Kevin Teich wrote:


This suggests that the number of values in the .mgh file is different
than the number of vertices in the surface. Did you regenerate the
surface after generating the .mgh file?

On Sun, 2007-05-13 at 15:29 -0400, Catherine Hartley wrote:

Hi,

I'm having a problem with the development version of tksurfer.  When
I try to load a sig.mgh file as an overlay, I get the following error:

% surfer: couldn't load /Applications/freesurfer/subjects/reruns/
glmleft/ReappCSplusContrast/sig.mgh
sclv_read_from_volume: error in FunD_New

Thanks,
Cate
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[Freesurfer] Failure of mri_aparc2aseg

2007-05-14 Thread Goldman, Aaron (NIH/NIMH) [C]

Hi, I just ran mri_aparc2aseg on a group of subjects, and a couple of them 
failed to produce an output file despite lacking any apparent error messages. 
The command I ran was (with subj name replaced):

mri_aparc2aseg --s ## --o aparc_cor+aseg.mgz --ribbon --annot final

These are subjects whose aparcs have been edited, but still have only the 
standard set of labels. The screen output for one that failed was:

SUBJECTS_DIR /j/rstruc2/surfaces/sibstudy/nc
subject ##
outvol aparc_cor+aseg.mgz
useribbon 1
baseoffset 0

Reading lh white surface
 /j/rstruc2/surfaces/sibstudy/nc/##/surf/lh.white

Building hash of lh white

Reading lh pial surface
 /j/rstruc2/surfaces/sibstudy/nc/##/surf/lh.pial

Building hash of lh pial

Loading lh annotations from 
/j/rstruc2/surfaces/sibstudy/nc/##/label/lh.final.annot
reading colortable from annotation file...
colortable with 35 entries read (originally 
/autofs/space/birn_044/users/buckner_surf_atlas_rebuild/scripts/colortable_final.txt)

Reading rh white surface
 /j/rstruc2/surfaces/sibstudy/nc/##/surf/rh.white

Building hash of rh white

Reading rh pial surface
 /j/rstruc2/surfaces/sibstudy/nc/##/surf/rh.pial

Building hash of rh pial

Loading rh annotations from 
/j/rstruc2/surfaces/sibstudy/nc/##/label/rh.final.annot
reading colortable from annotation file...
colortable with 35 entries read (originally 
/autofs/space/birn_044/users/buckner_surf_atlas_rebuild/scripts/colortable_final.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading lh ribbon mask from 
/j/rstruc2/surfaces/sibstudy/nc/##/mri/lh.ribbon.mgz
  Talairach transform 
/data1/c/brad/subjects/surfaces/##/mri/transforms/talairach.xfm does not 
exist...
Loading tal xfm file 
/j/rstruc2/surfaces/sibstudy/nc/##/mri/transforms/talairach.xfm
Loading rh ribbon mask from 
/j/rstruc2/surfaces/sibstudy/nc/##/mri/rh.ribbon.mgz
  Talairach transform 
/data1/c/brad/subjects/surfaces/##/mri/transforms/talairach.xfm does not 
exist...
Loading tal xfm file 
/j/rstruc2/surfaces/sibstudy/nc/##/mri/transforms/talairach.xfm

Loading aseg from /j/rstruc2/surfaces/sibstudy/nc/##/mri/aseg.mgz
  Talairach transform 
/data1/c/brad/subjects/surfaces/##/mri/transforms/talairach.xfm does not 
exist...
Loading tal xfm file 
/j/rstruc2/surfaces/sibstudy/nc/##/mri/transforms/talairach.xfm
ASeg Vox2RAS: ---
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
-

Labeling Slice
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
140 141 142
aseg id = 3
crs = 142 142 158, ras = -14. 30. -14.
lhw  122604  2.06939 -15.8773  30.8370  -14.2401
lhp  122604  0.63675 -13.6225  29.9035  -14.5036
rhp  122694  13.50887 -0.9827  29.1451  -10.4915
annot = 0, annotid = -1
  0  unknown  25   5  25   0
  1  bankssts 25 100  40   0
  2  caudalanteriorcingulate 125 100 160   0
  3  caudalmiddlefrontal 100  25   0   0
  4  corpuscallosum  120  70  50   0
  5  cuneus  220  20 100   0
  6  entorhinal  220  20  10   0
  7  fusiform180 220 140   0
  8  inferiorparietal220  60 220   0
  9  inferiortemporal180  40 120   0
 10  isthmuscingulate140  20 140   0
 11  lateraloccipital 20  30 140   0
 12  lateralorbitofrontal 35  75  50   0
 13  lingual 225 140 140   0
 14  medialorbitofrontal 200  35  75   0
 15  middletemporal  160 100  50   0
 16  parahippocampal  20 220  60   0
 17  paracentral  60 220  60   0
 18  parsopercularis 220 180 140   0
 19  parsorbitalis20 100  50   0
 20  parstriangularis220  60  20   0
 21  pericalcarine   120 100  60   0
 22  postcentral 220  20  20   0
 23  posteriorcingulate  220 180 220   0
 24  precentral   60  20 220   0
 25  precuneus   160 140 180   0
 26  rostralanteriorcingulate 80  20 140   0
 27  rostralmiddlefrontal 75  50 125   0
 28  superiorfrontal  20 220 160   0
 29  superiorparietal

RE: [Freesurfer] Failure of mri_aparc2aseg

2007-05-14 Thread Goldman, Aaron (NIH/NIMH) [C]

Okay, never mind. It turned out there were a couple nodes without labels
that'd been screwing things up.

Thanks,

-Aaron-

-Original Message-
From: Goldman, Aaron (NIH/NIMH) [C] 
Sent: Monday, May 14, 2007 4:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Failure of mri_aparc2aseg

Hi, I just ran mri_aparc2aseg on a group of subjects, and a couple of
them failed to produce an output file despite lacking any apparent error
messages. The command I ran was (with subj name replaced):

mri_aparc2aseg --s ## --o aparc_cor+aseg.mgz --ribbon --annot final

These are subjects whose aparcs have been edited, but still have only
the standard set of labels. The screen output for one that failed was:

SUBJECTS_DIR /j/rstruc2/surfaces/sibstudy/nc
subject ##
outvol aparc_cor+aseg.mgz
useribbon 1
baseoffset 0

Reading lh white surface
 /j/rstruc2/surfaces/sibstudy/nc/##/surf/lh.white

Building hash of lh white

Reading lh pial surface
 /j/rstruc2/surfaces/sibstudy/nc/##/surf/lh.pial

Building hash of lh pial

Loading lh annotations from
/j/rstruc2/surfaces/sibstudy/nc/##/label/lh.final.annot
reading colortable from annotation file...
colortable with 35 entries read (originally
/autofs/space/birn_044/users/buckner_surf_atlas_rebuild/scripts/colortab
le_final.txt)

Reading rh white surface
 /j/rstruc2/surfaces/sibstudy/nc/##/surf/rh.white

Building hash of rh white

Reading rh pial surface
 /j/rstruc2/surfaces/sibstudy/nc/##/surf/rh.pial

Building hash of rh pial

Loading rh annotations from
/j/rstruc2/surfaces/sibstudy/nc/##/label/rh.final.annot
reading colortable from annotation file...
colortable with 35 entries read (originally
/autofs/space/birn_044/users/buckner_surf_atlas_rebuild/scripts/colortab
le_final.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading lh ribbon mask from
/j/rstruc2/surfaces/sibstudy/nc/##/mri/lh.ribbon.mgz
  Talairach transform
/data1/c/brad/subjects/surfaces/##/mri/transforms/talairach.xfm does
not exist...
Loading tal xfm file
/j/rstruc2/surfaces/sibstudy/nc/##/mri/transforms/talairach.xfm
Loading rh ribbon mask from
/j/rstruc2/surfaces/sibstudy/nc/##/mri/rh.ribbon.mgz
  Talairach transform
/data1/c/brad/subjects/surfaces/##/mri/transforms/talairach.xfm does
not exist...
Loading tal xfm file
/j/rstruc2/surfaces/sibstudy/nc/##/mri/transforms/talairach.xfm

Loading aseg from /j/rstruc2/surfaces/sibstudy/nc/##/mri/aseg.mgz
  Talairach transform
/data1/c/brad/subjects/surfaces/##/mri/transforms/talairach.xfm does
not exist...
Loading tal xfm file
/j/rstruc2/surfaces/sibstudy/nc/##/mri/transforms/talairach.xfm
ASeg Vox2RAS: ---
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
-

Labeling Slice
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17
18  19
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37
38  39
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57
58  59
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77
78  79
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97
98  99
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117
118 119
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137
138 139
140 141 142
aseg id = 3
crs = 142 142 158, ras = -14. 30. -14.
lhw  122604  2.06939 -15.8773  30.8370  -14.2401
lhp  122604  0.63675 -13.6225  29.9035  -14.5036
rhp  122694  13.50887 -0.9827  29.1451  -10.4915
annot = 0, annotid = -1
  0  unknown  25   5  25   0
  1  bankssts 25 100  40   0
  2  caudalanteriorcingulate 125 100 160   0
  3  caudalmiddlefrontal 100  25   0   0
  4  corpuscallosum  120  70  50   0
  5  cuneus  220  20 100   0
  6  entorhinal  220  20  10   0
  7  fusiform180 220 140   0
  8  inferiorparietal220  60 220   0
  9  inferiortemporal180  40 120   0
 10  isthmuscingulate140  20 140   0
 11  lateraloccipital 20  30 140   0
 12  lateralorbitofrontal 35  75  50   0
 13  lingual 225 140 140   0
 14  medialorbitofrontal 200  35  75   0
 15  middletemporal  160 100  50   0
 16  parahippocampal  20 220  60   0
 17  paracentral  60 220  60   0
 18  parsopercularis 220 180 140   0
 19  parsorbitalis20 100  50   0
 20  parstriangularis220  60  20   0
 21  pericalcarine   120 100  60   0
 22  postcentral 220  20  20   0
 23  posteriorcingulate  220 180 220   0
 24  precentra

[Freesurfer] reg-feat2anat regsitration problems

2007-05-14 Thread [EMAIL PROTECTED]

Hi Doug & others,
   
  I am trying to use reg-feat2anat as it is described on the FSL web page:
  http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html
   
  However, I always seem t get a very bad registration. I tried using different 
values for  --maxangle --cost mutualinfo --bins, but maintained --dof always at 
6 for rigid body registration of the T1 and EPI, but didn't gt any good results.
  Initially I thought it might be because reg-fea2anat does not use a 
skull-stripped T1, but  when I run Feat using the T1.mgz (converted to .nii.gz) 
as the main structural image for Registration (and the MNI brain as standard 
space), both with 'Full Search' option and dof = 6, the registration (with 
FEAT)  works well. 
  Is there anything else I can try to make it work with reg-feat2anat. Why 
wouldn't the registration work on my data with reg-feat2anat given that it 
works with Feat?
   
  Any comments or suggestions would be very appreciated.
   
  best,
  
Sandy

   
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Re: [Freesurfer] reg-feat2anat regsitration problems

2007-05-14 Thread Doug Greve

can you send the information described in 
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?


doug

[EMAIL PROTECTED] wrote:


Hi Doug & others,
 
I am trying to use reg-feat2anat as it is described on the FSL web page:

http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html
 
However, I always seem t get a very bad registration. I tried 
using different values for  --maxangle --cost mutualinfo --bins, but 
maintained --dof always at 6 for rigid body registration of the T1 and 
EPI, but didn't gt any good results.
Initially I thought it might be because reg-fea2anat does not use a 
skull-stripped T1, but  when I run Feat using the T1.mgz (converted to 
.nii.gz) as the main structural image for Registration (and the MNI 
brain as standard space), both with 'Full Search' option and dof = 6, 
the registration (with FEAT)  works well.
Is there anything else I can try to make it work with reg-feat2anat. 
Why wouldn't the registration work on my data with reg-feat2anat given 
that it works with Feat?
 
Any comments or suggestions would be very appreciated.
 
best,


Sandy


Be a better Heartthrob. Get better relationship answers 
from 
someone who knows.

Yahoo! Answers - Check it out.



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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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[Freesurfer] binary masks: 1 output file per aseg label

2007-05-14 Thread Juranek, Jenifer

I'm interested in parsing aseg.mgz into separate binary mask files for
each aseg label. Is this possible? The closest topic I found was located
at the following URL:

 

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFu
nctionalSpace


2.0 Creating binary masks


The segmentation for a particular structure can be extracted to create a
binary mask (i.e., a volume where the voxel value is 1 if it is in the
structure and 0 otherwise). To make a binary mask of the left putamen,
which has been assigned label 12 (see
${FREESURFER_HOME}/FreeSurferColorLUT.txt), use the following command: 

avwmaths ./fbert.feat/reg/freesurfer/aparc+aseg.nii.gz \
-thr 12 -uthr 12 \
./fbert.feat/reg/freesurfer/lh.putamen.nii.gz

 

I checked the following for additional help...but still need some
help...

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommands

 

Many Thanks,

Jenifer

 

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Re: [Freesurfer] binary masks: 1 output file per aseg label

2007-05-14 Thread Bruce Fischl


Hi Jenifer,

yes, you could do that for each label defined in the aseg.stats file (or 
the FreeSurferColorLUT.txt, but that will contain labels that don't exist 
in that volume).


what else are you trying to do that you need help with?

Bruce

On Mon, 14 May 2007, Juranek, Jenifer  wrote:


I'm interested in parsing aseg.mgz into separate binary mask files for
each aseg label. Is this possible? The closest topic I found was located
at the following URL:



http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFu
nctionalSpace


2.0 Creating binary masks


The segmentation for a particular structure can be extracted to create a
binary mask (i.e., a volume where the voxel value is 1 if it is in the
structure and 0 otherwise). To make a binary mask of the left putamen,
which has been assigned label 12 (see
${FREESURFER_HOME}/FreeSurferColorLUT.txt), use the following command:

avwmaths ./fbert.feat/reg/freesurfer/aparc+aseg.nii.gz \
   -thr 12 -uthr 12 \
   ./fbert.feat/reg/freesurfer/lh.putamen.nii.gz



I checked the following for additional help...but still need some
help...

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommands



Many Thanks,

Jenifer





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Re: [Freesurfer] binary masks: 1 output file per aseg label

2007-05-14 Thread Doug Greve

You can also use mri_binarize (it takes any format as input). We don't 
have anything that will automatically generate a separate volume for 
each label.


Bruce Fischl wrote:


Hi Jenifer,

yes, you could do that for each label defined in the aseg.stats file 
(or the FreeSurferColorLUT.txt, but that will contain labels that 
don't exist in that volume).


what else are you trying to do that you need help with?

Bruce

On Mon, 14 May 2007, Juranek, Jenifer  wrote:


I'm interested in parsing aseg.mgz into separate binary mask files for
each aseg label. Is this possible? The closest topic I found was located
at the following URL:



http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFu
nctionalSpace


2.0 Creating binary masks


The segmentation for a particular structure can be extracted to create a
binary mask (i.e., a volume where the voxel value is 1 if it is in the
structure and 0 otherwise). To make a binary mask of the left putamen,
which has been assigned label 12 (see
${FREESURFER_HOME}/FreeSurferColorLUT.txt), use the following command:

avwmaths ./fbert.feat/reg/freesurfer/aparc+aseg.nii.gz \
   -thr 12 -uthr 12 \
   ./fbert.feat/reg/freesurfer/lh.putamen.nii.gz



I checked the following for additional help...but still need some
help...

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommands



Many Thanks,

Jenifer





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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] binary masks: 1 output file per aseg label

2007-05-14 Thread David Perlman


On May 14, 2007, at 6:28 PM, Juranek, Jenifer wrote:

I’m interested in parsing aseg.mgz into separate binary mask files  
for each aseg label. Is this possible? The closest topic I found  
was located at the following URL:


...
I checked the following for additional help…but still need some help…

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommands


Here's a bash script that will automatically read through the  
aseg.stats file and run the "avwmaths" command for each segment.  Put  
the stuff between the lines into a text file, call it something like  
aseg-breakout.sh, and run it with source aseg-breakout.sh subject- 
name edited-aseg.stats.  I recommend you cut out only the lines you  
want from aseg-stats; if you run it on the whole thing it will  
generate about 685 output files at about 1 megabyte each on average  
which is a lot of data to fill your computer with.  But hey, so is  
freesurfer.


Also, run it as is to make sure it finds the ones you want; then edit  
this file to remove the word "echo" and run it again to actually do it.


I haven't tested this live, but if the avwmaths command works as  
given, this should work too.


Maybe you need to do everything with a .nii.gz extension instead of  
mgz, I don't know.  If you need to do that, just replace ".mgz" with  
".nii.gz" everywhere in this script.


If you want to know how this works, here is an excellent and  
extremely detailed guide to bash scripts:

http://tldp.org/LDP/abs/html/


--cut here
#!/bin/bash
# Usage: ./$0 subject-name aseg.stats
# if $SUBJECTS_DIR is set properly,
# it will know where to find the stats and the aparc+aseg.mgz
# if you don't want to do all the segs in aseg.stats,
# make a copy of the file with just the lines you want
# and give that as input to this script

statsfile="${SUBJECTS_DIR}/${1}/stats/${2}"
asegfile="${SUBJECTS_DIR}/${1}/mri/aparc+aseg.mgz"
outputdir="${SUBJECTS_DIR}/${1}/mri/segmasks"

mkdir ${outputdir}	# make a directory for all these output files to  
go into


outputextension=".mgz"# or whatever, .nii.gz would work too

while read theline; do  # read one line from aseg.stat

linearray=( ${theline} )# parse the columns into an 
array
if [[ ${linearray[0]:0:1} == '#' ]]; then
:   # do nothing, skip the lines where first character is #
# because they are comments
else
threshold=${linearray[1]}   # the intensity value of the 
segment
segname=${linearray[4]} # the name of the segment
echo avwmaths asegfile \
-thr ${threshold} -uthr ${threshold} \
${outputdir}/${segname}${outputextension}
fi

done <${statsfile}	# read input from the aseg.stats file or whatever  
is specified


--cut here


--
-dave
After all, it is not *that* inexpressible.
-H.H. The Dalai Lama




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[Freesurfer] Topological defects

2007-05-14 Thread Juergen Haenggi

Dear Freesurfer users

Is there any rule of thumb with respect to the size of topological defects?
Sometimes large defects (involving more than 1 or 2 vertices) occur
and the topological correction for these defects runs more than 48 hours and
sometimes failed to correct them. How long should I wait? Up to which number
of vertices involved in a defect I should accept it or manually edit it?

Thanks a lot for help
Best regards
Juergen

---
Juergen Haenggi
Ph.D. (Dr. des.)
Division of Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
[EMAIL PROTECTED] (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)
---



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[Freesurfer] reg- feat2anat error

Re: [Freesurfer] Make_average_subject error

Re: [Freesurfer] Make_average_subject error

[Freesurfer] (no subject)

[Freesurfer] question about 'mris_wm_volume: error while loading shared libraries: libstdc++.so.6'

Re: [Freesurfer] question about 'mris_wm_volume: error while loading shared libraries: libstdc++.so.6'

Re: [Freesurfer] question about 'mris_wm_volume: error whileloading shared libraries: libstdc++.so.6'

Re: [Freesurfer] quick scatterplot label question

Re: [Freesurfer] can't load sig.mgh in dev tksurfer

Re: [Freesurfer] can't load sig.mgh in dev tksurfer

Re: [Freesurfer] question about 'mris_wm_volume: error whileloading shared libraries: libstdc++.so.6'

Re: [Freesurfer] question about 'mris_wm_volume: errorwhileloading shared libraries: libstdc++.so.6'

Re: [Freesurfer] question about 'mris_wm_volume: errorwhileloading shared libraries: libstdc++.so.6'

Re: [Freesurfer] question about 'mris_wm_volume: errorwhileloading shared libraries: libstdc++.so.6'

Re: [Freesurfer] reg- feat2anat error

Re: [Freesurfer] question about 'mris_wm_volume: errorwhileloadingshared libraries: libstdc++.so.6'

[Freesurfer] surf-sess error

Re: [Freesurfer] can't load sig.mgh in dev tksurfer

Re: [Freesurfer] can't load sig.mgh in dev tksurfer

[Freesurfer] Failure of mri_aparc2aseg

RE: [Freesurfer] Failure of mri_aparc2aseg

[Freesurfer] reg-feat2anat regsitration problems

Re: [Freesurfer] reg-feat2anat regsitration problems

[Freesurfer] binary masks: 1 output file per aseg label

Re: [Freesurfer] binary masks: 1 output file per aseg label

Re: [Freesurfer] binary masks: 1 output file per aseg label

Re: [Freesurfer] binary masks: 1 output file per aseg label

[Freesurfer] Topological defects

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