Hi, I load Version 4.0,5, and it works!!!!!!!!!!!!! Thanks!!!
Yet, I just have another question now: Is it possible to
conduct a conjunction analysis like implemented in SPM5?
If not, is it valid to simply take the p-maps in the surface space and
compute the pooled dependent p-values according to Heller et. al 2007
(NeuroImage 37 1178-1185),
and if so are there Matlab readers for the p-map files?
thanks, schüss
-----Ursprüngliche Nachricht-----
Von: [EMAIL PROTECTED] im Auftrag von [EMAIL PROTECTED]
Gesendet: Mi 23.07.2008 23:31
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Freesurfer Digest, Vol 53, Issue 23
Send Freesurfer mailing list submissions to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Version 4.0.4 (Tricia Merkley)
2. AW: [Fsdev] Re: [Freesurfer] Talairach Coordinates
(Steinmann, Iris)
3. Vertex information lookup (P?draig Kitterick)
4. qdec ERROR: Rendering vtkXOpenGLRenderWindow (Juranek, Jenifer )
5. tkmedit problem with XQuartz-2.3.0 (Martin Kavec)
6. Re: qdec ERROR: Rendering vtkXOpenGLRenderWindow (Nick Schmansky)
7. Re: tkmedit problem with XQuartz-2.3.0 (Nick Schmansky)
8. RE: qdec ERROR: Rendering vtkXOpenGLRenderWindow
(Juranek, Jenifer )
9. RE: qdec ERROR: Rendering vtkXOpenGLRenderWindow (Nick Schmansky)
10. Re: tkmedit problem with XQuartz-2.3.0 (Martin Kavec)
----------------------------------------------------------------------
Message: 1
Date: Tue, 22 Jul 2008 14:59:54 -0700 (PDT)
From: Tricia Merkley <[EMAIL PROTECTED]>
Subject: [Freesurfer] Version 4.0.4
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
We ran several subjects using version 4.0.4 and now need to reinstall
freesurfer to finish the processing. Is there a linux centos4, 32 bit version
available somewhere?
Thanks,
Tricia Merkley
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------------------------------
Message: 2
Date: Wed, 23 Jul 2008 11:41:38 +0200
From: "Steinmann, Iris" <[EMAIL PROTECTED]>
Subject: AW: [Fsdev] Re: [Freesurfer] Talairach Coordinates
To: "Nick Schmansky" <[EMAIL PROTECTED]>, "Bruce Fischl"
<[EMAIL PROTECTED]>
Cc: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I have the Version 4.0.1. I will download v4.0.5 and try it again...
thank you!
-----Ursprüngliche Nachricht-----
Von: Nick Schmansky [mailto:[EMAIL PROTECTED]
Gesendet: Di 22.07.2008 15:58
An: Bruce Fischl
Cc: Steinmann, Iris; Freesurfer Mailing List
Betreff: Re: [Fsdev] Re: [Freesurfer] Talairach Coordinates
Iris,
I think this bug was fixed in v4.0.3. We can also just post tkmedit for
you to download if you tell me your distribution, ie, type:
cat $FREESURFER_HOME/build-stamp.txt
Nick
On Tue, 2008-07-22 at 09:47 -0400, Bruce Fischl wrote:
> Hi Iris,
>
> what version are you using? I tracked down and fixed a bug like this some
> time (a year?) ago.
>
> cheers,
> Bruce
> On Tue, 22 Jul 2008, Steinmann, Iris wrote:
>
> >
> > Dear FreeSurfers
> >
> > I use the command: <tkmedit-sess -s vpnXY -aparc+aseg -analysis ampmod -c
> > AmvsSIN> and want to mark a point at special Talairach coordinates at this
> > brain. When I type in the coordinates e.g. -46 -19 8 and press RETURN the
> > the Numbers change to e.g.
> > -46 -92 15. I dont found a possibility to mark the talairach coordinates I
> > want. Can you help me?
> > Thanks!
> >
> > Iris
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> _______________________________________________
> Fsdev mailing list
> [EMAIL PROTECTED]
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fsdev
>
>
------------------------------
Message: 3
Date: Wed, 23 Jul 2008 15:05:14 +0100
From: P?draig Kitterick <[EMAIL PROTECTED]>
Subject: [Freesurfer] Vertex information lookup
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear list,
I wish to obtain information about a list of surface vertices, including
their coordinates in MNI305 and Talairach spaces. Is there any tool that
can provide this information at the command line? I can get the
information by loading tksurfer and selecting the vertex, but this is
slow for a long list of ROIs.
I have found that the mris_info tool will give me the real coordinate of
a surface vertex, but there is a discrepency between the information it
provides and that obtained from tksurfer. For example, for a certain
vertex, mris_info gives the coordinate (25.2, -93.5, 12.5). Loading the
surface into tksurfer and selecting the same vertex gives a location of
(24.90, -93.27, 12.26). The locations are obviously close, but the
difference can't just be due to rounding errors.
Padraig
--
Pádraig Kitterick
Graduate Student
Department of Psychology
University of York
Heslington
York YO10 5DD
UK
Tel: +44 (0) 1904 43 3170
Email: [EMAIL PROTECTED]
------------------------------
Message: 4
Date: Wed, 23 Jul 2008 11:14:48 -0500
From: "Juranek, Jenifer " <[EMAIL PROTECTED]>
Subject: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
Running Freesurfer v405 on RHEL5. Tried to launch qdec from the command prompt.
While the splash screen did appear with the inflated brain surface, the qdec
interface did not appear (even after 10min). When I tried to CTRL-C the
terminal window, the following error message appeared:
[EMAIL PROTECTED] subjects]$ qdec &
ERROR: In
/usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx,
line 219
vtkXOpenGLRenderWindow (0x7e06290): Could not find a decent visual
[EMAIL PROTECTED] subjects]$ ps -ef | grep qdec
jjuranek 32682 32579 0 10:45 pts/11 00:00:00 /bin/tcsh -ef
/usr/local/freesurfer/bin/qdec
jjuranek 32687 32682 0 10:45 pts/11 00:00:00 qdec.bin
jjuranek 32763 9505 0 11:13 pts/1 00:00:00 grep qdec
[EMAIL PROTECTED] subjects]$ kill -1 32687
Any ideas how to fix?
Thanks,
Jenifer
------------------------------
Message: 5
Date: Wed, 23 Jul 2008 22:43:15 +0200
From: Martin Kavec <[EMAIL PROTECTED]>
Subject: [Freesurfer] tkmedit problem with XQuartz-2.3.0
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="us-ascii"
Hi,
On my macbook pro (MAC OS X 10.5) I have recently updated my X to 2.3.0 and
now I can not launch tkmedit:
$ tkmedit $SUBJ brainmask.mgz rh.white -aux-surface lh.white
Converting main surface: 100% done.
Converting main surface: 100% done.
Converting original surface: 100% done.
Converting pial surface: 100% done.
Converting main surface: 100% done.
Converting main surface: 100% done.
Converting original surface: 100% done.
Converting pial surface: 100% done.
Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl
Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl
X Error of failed request: BadValue (integer parameter out of range for
operation)
Major opcode of failed request: 45 (X_OpenFont)
Value in failed request: 0xe00004
Serial number of failed request: 33
Current serial number in output stream: 34
$
Thanks,
Martin
------------------------------
Message: 6
Date: Wed, 23 Jul 2008 16:47:54 -0400
From: Nick Schmansky <[EMAIL PROTECTED]>
Subject: Re: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
To: "Juranek, Jenifer" <[EMAIL PROTECTED]>
Cc: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain
Jenifer,
Is this new to v405, or have prior versions also had this problem?
Are you running directly from the terminal? Or over an ssh or vnc
connection? If over vnc, from what kind of machine?
Nick
On Wed, 2008-07-23 at 11:14 -0500, Juranek, Jenifer wrote:
> Hi,
> Running Freesurfer v405 on RHEL5. Tried to launch qdec from the command
> prompt. While the splash screen did appear with the inflated brain surface,
> the qdec interface did not appear (even after 10min). When I tried to CTRL-C
> the terminal window, the following error message appeared:
>
> [EMAIL PROTECTED] subjects]$ qdec &
> ERROR: In
> /usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx,
> line 219
> vtkXOpenGLRenderWindow (0x7e06290): Could not find a decent visual
>
> [EMAIL PROTECTED] subjects]$ ps -ef | grep qdec
> jjuranek 32682 32579 0 10:45 pts/11 00:00:00 /bin/tcsh -ef
> /usr/local/freesurfer/bin/qdec
> jjuranek 32687 32682 0 10:45 pts/11 00:00:00 qdec.bin
> jjuranek 32763 9505 0 11:13 pts/1 00:00:00 grep qdec
> [EMAIL PROTECTED] subjects]$ kill -1 32687
>
> Any ideas how to fix?
>
> Thanks,
> Jenifer
>
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
------------------------------
Message: 7
Date: Wed, 23 Jul 2008 16:50:01 -0400
From: Nick Schmansky <[EMAIL PROTECTED]>
Subject: Re: [Freesurfer] tkmedit problem with XQuartz-2.3.0
To: Martin Kavec <[EMAIL PROTECTED]>
Cc: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain
Martin,
>From where did the X update originate? tkmedit is known to work on mac
os 10.5 using the default X setup.
Nick
On Wed, 2008-07-23 at 22:43 +0200, Martin Kavec wrote:
> Hi,
>
> On my macbook pro (MAC OS X 10.5) I have recently updated my X to 2.3.0 and
> now I can not launch tkmedit:
>
> $ tkmedit $SUBJ brainmask.mgz rh.white -aux-surface lh.white
> Converting main surface: 100% done.
> Converting main surface: 100% done.
> Converting original surface: 100% done.
> Converting pial surface: 100% done.
> Converting main surface: 100% done.
> Converting main surface: 100% done.
> Converting original surface: 100% done.
> Converting pial surface: 100% done.
> Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl
> Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl
> Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl
> Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl
> X Error of failed request: BadValue (integer parameter out of range for
> operation)
> Major opcode of failed request: 45 (X_OpenFont)
> Value in failed request: 0xe00004
> Serial number of failed request: 33
> Current serial number in output stream: 34
> $
>
> Thanks,
>
> Martin
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
------------------------------
Message: 8
Date: Wed, 23 Jul 2008 15:51:11 -0500
From: "Juranek, Jenifer " <[EMAIL PROTECTED]>
Subject: RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
To: "Nick Schmansky" <[EMAIL PROTECTED]>
Cc: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi Nick,
This is the first time I have tried to use the qdec feature, so I am unable to
report whether new problem to v405 or not.
I am running from the terminal window on the RHEL5 box (not across VPN or SSH
or VNC).
Thanks for any help you can provide,
Jenifer
-----Original Message-----
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Wed 7/23/2008 3:47 PM
To: Juranek, Jenifer
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
Jenifer,
Is this new to v405, or have prior versions also had this problem?
Are you running directly from the terminal? Or over an ssh or vnc
connection? If over vnc, from what kind of machine?
Nick
On Wed, 2008-07-23 at 11:14 -0500, Juranek, Jenifer wrote:
> Hi,
> Running Freesurfer v405 on RHEL5. Tried to launch qdec from the command
> prompt. While the splash screen did appear with the inflated brain surface,
> the qdec interface did not appear (even after 10min). When I tried to CTRL-C
> the terminal window, the following error message appeared:
>
> [EMAIL PROTECTED] subjects]$ qdec &
> ERROR: In
> /usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx,
> line 219
> vtkXOpenGLRenderWindow (0x7e06290): Could not find a decent visual
>
> [EMAIL PROTECTED] subjects]$ ps -ef | grep qdec
> jjuranek 32682 32579 0 10:45 pts/11 00:00:00 /bin/tcsh -ef
> /usr/local/freesurfer/bin/qdec
> jjuranek 32687 32682 0 10:45 pts/11 00:00:00 qdec.bin
> jjuranek 32763 9505 0 11:13 pts/1 00:00:00 grep qdec
> [EMAIL PROTECTED] subjects]$ kill -1 32687
>
> Any ideas how to fix?
>
> Thanks,
> Jenifer
>
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
------------------------------
Message: 9
Date: Wed, 23 Jul 2008 17:04:17 -0400
From: Nick Schmansky <[EMAIL PROTECTED]>
Subject: RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
To: "Juranek, Jenifer" <[EMAIL PROTECTED]>
Cc: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain
Jenifer,
In the file /etc/X11/xorg.conf, within the section titled Section
"Module", make sure this line exists:
Load "glx"
You might need to have your administrator perform this change, as it
requires root access. You will have to restart your X server after
making this change (Ctrl-Bksp).
Nick
On Wed, 2008-07-23 at 15:51 -0500, Juranek, Jenifer wrote:
> Hi Nick,
> This is the first time I have tried to use the qdec feature, so I am unable
> to report whether new problem to v405 or not.
>
> I am running from the terminal window on the RHEL5 box (not across VPN or SSH
> or VNC).
>
> Thanks for any help you can provide,
> Jenifer
>
> -----Original Message-----
> From: Nick Schmansky [mailto:[EMAIL PROTECTED]
> Sent: Wed 7/23/2008 3:47 PM
> To: Juranek, Jenifer
> Cc: Freesurfer Mailing List
> Subject: Re: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
>
> Jenifer,
>
> Is this new to v405, or have prior versions also had this problem?
>
> Are you running directly from the terminal? Or over an ssh or vnc
> connection? If over vnc, from what kind of machine?
>
> Nick
>
>
> On Wed, 2008-07-23 at 11:14 -0500, Juranek, Jenifer wrote:
> > Hi,
> > Running Freesurfer v405 on RHEL5. Tried to launch qdec from the command
> > prompt. While the splash screen did appear with the inflated brain surface,
> > the qdec interface did not appear (even after 10min). When I tried to
> > CTRL-C the terminal window, the following error message appeared:
> >
> > [EMAIL PROTECTED] subjects]$ qdec &
> > ERROR: In
> > /usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx,
> > line 219
> > vtkXOpenGLRenderWindow (0x7e06290): Could not find a decent visual
> >
> > [EMAIL PROTECTED] subjects]$ ps -ef | grep qdec
> > jjuranek 32682 32579 0 10:45 pts/11 00:00:00 /bin/tcsh -ef
> > /usr/local/freesurfer/bin/qdec
> > jjuranek 32687 32682 0 10:45 pts/11 00:00:00 qdec.bin
> > jjuranek 32763 9505 0 11:13 pts/1 00:00:00 grep qdec
> > [EMAIL PROTECTED] subjects]$ kill -1 32687
> >
> > Any ideas how to fix?
> >
> > Thanks,
> > Jenifer
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
>
>
>
------------------------------
Message: 10
Date: Wed, 23 Jul 2008 23:09:35 +0200
From: Martin Kavec <[EMAIL PROTECTED]>
Subject: Re: [Freesurfer] tkmedit problem with XQuartz-2.3.0
To: Nick Schmansky <[EMAIL PROTECTED]>
Cc: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-6"
Hi Nick,
the update comes from:
http://xquartz.macosforge.org/trac/wiki
My other X (KDE) applications continue working, and FSL (Tcl/Tk GUI) works
fine too.
Thanks,
Martin
On Wednesday 23 July 2008 22:50:01 Nick Schmansky wrote:
> Martin,
>
> >From where did the X update originate? tkmedit is known to work on mac
>
> os 10.5 using the default X setup.
>
> Nick
>
> On Wed, 2008-07-23 at 22:43 +0200, Martin Kavec wrote:
> > Hi,
> >
> > On my macbook pro (MAC OS X 10.5) I have recently updated my X to 2.3.0
> > and now I can not launch tkmedit:
> >
> > $ tkmedit $SUBJ brainmask.mgz rh.white -aux-surface lh.white
> > Converting main surface: 100% done.
> > Converting main surface: 100% done.
> > Converting original surface: 100% done.
> > Converting pial surface: 100% done.
> > Converting main surface: 100% done.
> > Converting main surface: 100% done.
> > Converting original surface: 100% done.
> > Converting pial surface: 100% done.
> > Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl
> > Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl
> > Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl
> > Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl
> > X Error of failed request: BadValue (integer parameter out of range for
> > operation)
> > Major opcode of failed request: 45 (X_OpenFont)
> > Value in failed request: 0xe00004
> > Serial number of failed request: 33
> > Current serial number in output stream: 34
> > $
> >
> > Thanks,
> >
> > Martin
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
**********************************
Senior Clinical Research Associate
MRI Unit of the Department of Radiology
Erasme Hospital
Lennik Street 808
B-1070 Brussels
BELGIUM
tel: +32-2-555-4325
fax: +32-2-555-3994
email: [EMAIL PROTECTED]
**********************************
-----------------------------------------------
Find a way, or make one!
------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 53, Issue 23
******************************************
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