My subject's anatomical scan seems to be relatively well aligned with the fuzzy talairach brain, but the green 'orig' surface is completely off. How is this possible? Why do we need the surface at all if it's not used for alignment?
The tutorial advises using the 'final objective function value' from mritotal.log to determine if the registration is off before making any edits. If the registration needs to be modified, and if it's important to have an accurate talairach.xfm, how do I determine if it is aligned sufficiently after making edits?
Thanks, Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:23 PM >>>
Hit the "compare" button to flip back and forth between the talairach brain and your subjects anatomical.
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
How can I check the registration if I can't see the surface? -Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:07 PM >>>
If you don't have a surface, then don't run it with --surf. It's important to have an accurate talairach.xfm.
doug
On Mon, 17 Oct 2005, Sasha Wolosin wrote:
Dear Nick,
I recently installed the dev release from October 3rd, but
tkregister2 still does not work after autorecon1. (It will not load the orig volume because rh.orig and lh.orig do not yet exist in the surf folder for the subject) Am I not using the correct inputs for this step (my inputs are the same as that of the tutorial)? How important is it to have a correct registration before running autorecon2?
Here is the script for a subject who has only been run with
autorecon1:
% [root@bwy-1-113mm mri]$ tkregister2 --mgz --s 2333 --fstal --surf
orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.538; 0.000 0.000 1.000 -132.197; 0.000 -1.000 0.000 137.708; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; subject = 2333 Reading lh surface orig MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open
file
No such file or directory tkregister2: could not read surface orig No such file or directory [root@bwy-1-113mm mri]$
If I instead run the command:tkregister2 --mgz --s 2333 --fstal tkregister2 does load, but there is no green orig outline to guide
any corrections.
If I run tkregister2 after running autorecon2, it also loads, but
the registration is all wrong. (It was about as far off as the tutorial subject) Here is the output:
[root@bwy-1-113mm /freesurfer_subjects]$ tkregister2 --mgz --s 2338
--fstal --surf orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2338/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 136.359; 0.000 0.000 1.000 -135.309; -0.000 -1.000 0.000 159.346; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; subject = 2338 Reading lh surface orig Done reading surface Reading rh surface orig Done reading surface Zoom Factor = 2 FOV = 256 Opening window 2338 Setting scale tkregister2: interface: /freesurfer/lib/tcl/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change:
macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
Looking through the script I noticed it never mentions the path to
the correct .xfm file, which is in the subjects directory (the subjects directory is /freesurfer_subjects, not /freesurfer/subjects) But I copied the .xfm file to the folder it was looking for, and the registration was still just as far off.
Any help is greatly appreciated, Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Nick Schmansky nicks@nmr.mgh.harvard.edu 09/15/05 2:40 PM >>>
Sasha,
An alternative solution is to create the COR files for the
talairach
subject:
cd $SUBJECTS_DIR/talairach/mri mri_convert -it mgz -ot cor orig.mgz orig/
This will deposit COR files into the orig/ directory, and your
current
tkregister2 should then work.
We are recommending using .mgz files over the older COR format, and
are
still trying to make all the tools fully compliant.
A new 'dev' release containing the updated tkregister2 will be
posted in
the next couple days.
Nick
On Thu, 2005-09-15 at 14:26 -0400, Doug Greve wrote:
I just fixed this error. For those in the nmr center, the fix will
be
live tomorrow. For those outside, you can download a new Linux
version
from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Sasha Wolosin wrote:
Dear all,
I am having trouble running tkregister2.
I get an error when I run tkregister2 on a subject after running
autorecon1 (see below.) However, I also get an error when I run it on bert.
It seems tkregister2 is searching for COR files, but I am using
mgz format. Am I not using the correct flags?
My subjects directory contains the talairach subject included in
the dev release. Do I need to download talairach separately?
Here is the output for subject 2335 and bert: [root@bwy-1-113mm talairach]$ tkregister2 --mgz --s 2335 --fstal INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.002 0.050 -0.017 -3.539; -0.053 1.034 -0.076 -12.275; 0.014 0.081 1.091 -14.424; 0.000 0.000 0.000 1.000; corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /freesurfer/subjects/talairach/mri/orig as
0
[root@bwy-1-113mm subjects]$ tkregister2 --mgz --s bert --fstal INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.154 -0.024 0.046 -5.813; 0.014 0.941 0.131 -21.893; -0.048 -0.155 1.123 -0.730; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /freesurfer/subjects/talairach/mri/orig as
0
[root@bwy-1-113mm subjects]$
Any help is greatly appreciated.
Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
So the surface does not align with the anatomical?
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
My subject's anatomical scan seems to be relatively well aligned with the fuzzy talairach brain, but the green 'orig' surface is completely off. How is this possible? Why do we need the surface at all if it's not used for alignment?
The tutorial advises using the 'final objective function value' from mritotal.log to determine if the registration is off before making any edits. If the registration needs to be modified, and if it's important to have an accurate talairach.xfm, how do I determine if it is aligned sufficiently after making edits?
Thanks, Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:23 PM >>>
Hit the "compare" button to flip back and forth between the talairach brain and your subjects anatomical.
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
How can I check the registration if I can't see the surface? -Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:07 PM >>>
If you don't have a surface, then don't run it with --surf. It's important to have an accurate talairach.xfm.
doug
On Mon, 17 Oct 2005, Sasha Wolosin wrote:
Dear Nick,
I recently installed the dev release from October 3rd, but
tkregister2 still does not work after autorecon1. (It will not load the orig volume because rh.orig and lh.orig do not yet exist in the surf folder for the subject) Am I not using the correct inputs for this step (my inputs are the same as that of the tutorial)? How important is it to have a correct registration before running autorecon2?
Here is the script for a subject who has only been run with
autorecon1:
% [root@bwy-1-113mm mri]$ tkregister2 --mgz --s 2333 --fstal --surf
orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.538; 0.000 0.000 1.000 -132.197; 0.000 -1.000 0.000 137.708; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; subject = 2333 Reading lh surface orig MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open
file
No such file or directory tkregister2: could not read surface orig No such file or directory [root@bwy-1-113mm mri]$
If I instead run the command:tkregister2 --mgz --s 2333 --fstal tkregister2 does load, but there is no green orig outline to guide
any corrections.
If I run tkregister2 after running autorecon2, it also loads, but
the registration is all wrong. (It was about as far off as the tutorial subject) Here is the output:
[root@bwy-1-113mm /freesurfer_subjects]$ tkregister2 --mgz --s 2338
--fstal --surf orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2338/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 136.359; 0.000 0.000 1.000 -135.309; -0.000 -1.000 0.000 159.346; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; subject = 2338 Reading lh surface orig Done reading surface Reading rh surface orig Done reading surface Zoom Factor = 2 FOV = 256 Opening window 2338 Setting scale tkregister2: interface: /freesurfer/lib/tcl/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change:
macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
Looking through the script I noticed it never mentions the path to
the correct .xfm file, which is in the subjects directory (the subjects directory is /freesurfer_subjects, not /freesurfer/subjects) But I copied the .xfm file to the folder it was looking for, and the registration was still just as far off.
Any help is greatly appreciated, Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Nick Schmansky nicks@nmr.mgh.harvard.edu 09/15/05 2:40 PM >>>
Sasha,
An alternative solution is to create the COR files for the
talairach
subject:
cd $SUBJECTS_DIR/talairach/mri mri_convert -it mgz -ot cor orig.mgz orig/
This will deposit COR files into the orig/ directory, and your
current
tkregister2 should then work.
We are recommending using .mgz files over the older COR format, and
are
still trying to make all the tools fully compliant.
A new 'dev' release containing the updated tkregister2 will be
posted in
the next couple days.
Nick
On Thu, 2005-09-15 at 14:26 -0400, Doug Greve wrote:
I just fixed this error. For those in the nmr center, the fix will
be
live tomorrow. For those outside, you can download a new Linux
version
from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Sasha Wolosin wrote:
Dear all,
I am having trouble running tkregister2.
I get an error when I run tkregister2 on a subject after running
autorecon1 (see below.) However, I also get an error when I run it on bert.
It seems tkregister2 is searching for COR files, but I am using
mgz format. Am I not using the correct flags?
My subjects directory contains the talairach subject included in
the dev release. Do I need to download talairach separately?
Here is the output for subject 2335 and bert: [root@bwy-1-113mm talairach]$ tkregister2 --mgz --s 2335 --fstal INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.002 0.050 -0.017 -3.539; -0.053 1.034 -0.076 -12.275; 0.014 0.081 1.091 -14.424; 0.000 0.000 0.000 1.000; corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /freesurfer/subjects/talairach/mri/orig as
0
[root@bwy-1-113mm subjects]$ tkregister2 --mgz --s bert --fstal INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.154 -0.024 0.046 -5.813; 0.014 0.941 0.131 -21.893; -0.048 -0.155 1.123 -0.730; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /freesurfer/subjects/talairach/mri/orig as
0
[root@bwy-1-113mm subjects]$
Any help is greatly appreciated.
Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sasha,
We are updating our tutorial to make it clearer how and when to correct a bad talairach alignment. The tutorial assumed that recon-all - autorecon-all was run, which would have created surfaces (which might not have been fully correct, but good enough to check talairach alignment).
In your case, where just autorecon1 was run (which is perfectly reasonable) the surface files have not yet been created, so they cannot be used to help (the operative word being 'help') with checking the alignment. It helps to have the surface data only because when it is overlayed in tkregister2 over the fuzzy talairach model, it shows-up as the green outline, as shown in the tutorial, which makes it very easy to do the alignment in tkregister2.
However, in the case where the surface data is not present, the alignment task is more difficult, but not impossible. In tkregister2, with the '-surf orig' parameter excluded, toggle back and forth (with the compare button) between the subject and the taliarach and you can eyeball the rotation, sizing, alignment etc. The alignment needs to be good, but not perfect. You can also load the talairach volume as an auxilary volume in tkmedit, and compare against it that way (but that will only tell you if its badly aligned, only tkregister2 will allow you generate a transform file (transforms/talairach.xfm) to properly align your subject to talairach space).
Proper talairach alignment is necessary for several downstream steps. The next being the 2nd normalization step, to get the approximate location of the center of the brain and the approximate superior/inferior direction. It's also used in mri_fill to localize the corpus callosum and the pons, and can be used in the spherical transform to initialize with a tal xform.
Nick
On Tue, 2005-10-18 at 14:20 -0400, Doug Greve wrote:
So the surface does not align with the anatomical?
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
My subject's anatomical scan seems to be relatively well aligned with the fuzzy talairach brain, but the green 'orig' surface is completely off. How is this possible? Why do we need the surface at all if it's not used for alignment?
The tutorial advises using the 'final objective function value' from mritotal.log to determine if the registration is off before making any edits. If the registration needs to be modified, and if it's important to have an accurate talairach.xfm, how do I determine if it is aligned sufficiently after making edits?
Thanks, Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:23 PM >>>
Hit the "compare" button to flip back and forth between the talairach brain and your subjects anatomical.
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
How can I check the registration if I can't see the surface? -Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:07 PM >>>
If you don't have a surface, then don't run it with --surf. It's important to have an accurate talairach.xfm.
doug
On Mon, 17 Oct 2005, Sasha Wolosin wrote:
Dear Nick,
I recently installed the dev release from October 3rd, but
tkregister2 still does not work after autorecon1. (It will not load the orig volume because rh.orig and lh.orig do not yet exist in the surf folder for the subject) Am I not using the correct inputs for this step (my inputs are the same as that of the tutorial)? How important is it to have a correct registration before running autorecon2?
Here is the script for a subject who has only been run with
autorecon1:
% [root@bwy-1-113mm mri]$ tkregister2 --mgz --s 2333 --fstal --surf
orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.538; 0.000 0.000 1.000 -132.197; 0.000 -1.000 0.000 137.708; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; subject = 2333 Reading lh surface orig MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open
file
No such file or directory tkregister2: could not read surface orig No such file or directory [root@bwy-1-113mm mri]$
If I instead run the command:tkregister2 --mgz --s 2333 --fstal tkregister2 does load, but there is no green orig outline to guide
any corrections.
If I run tkregister2 after running autorecon2, it also loads, but
the registration is all wrong. (It was about as far off as the tutorial subject) Here is the output:
[root@bwy-1-113mm /freesurfer_subjects]$ tkregister2 --mgz --s 2338
--fstal --surf orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2338/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 136.359; 0.000 0.000 1.000 -135.309; -0.000 -1.000 0.000 159.346; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; subject = 2338 Reading lh surface orig Done reading surface Reading rh surface orig Done reading surface Zoom Factor = 2 FOV = 256 Opening window 2338 Setting scale tkregister2: interface: /freesurfer/lib/tcl/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change:
macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
Looking through the script I noticed it never mentions the path to
the correct .xfm file, which is in the subjects directory (the subjects directory is /freesurfer_subjects, not /freesurfer/subjects) But I copied the .xfm file to the folder it was looking for, and the registration was still just as far off.
Any help is greatly appreciated, Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
> Nick Schmansky nicks@nmr.mgh.harvard.edu 09/15/05 2:40 PM >>>
Sasha,
An alternative solution is to create the COR files for the
talairach
subject:
cd $SUBJECTS_DIR/talairach/mri mri_convert -it mgz -ot cor orig.mgz orig/
This will deposit COR files into the orig/ directory, and your
current
tkregister2 should then work.
We are recommending using .mgz files over the older COR format, and
are
still trying to make all the tools fully compliant.
A new 'dev' release containing the updated tkregister2 will be
posted in
the next couple days.
Nick
On Thu, 2005-09-15 at 14:26 -0400, Doug Greve wrote:
I just fixed this error. For those in the nmr center, the fix will
be
live tomorrow. For those outside, you can download a new Linux
version
from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Sasha Wolosin wrote:
Dear all,
I am having trouble running tkregister2.
I get an error when I run tkregister2 on a subject after running
autorecon1 (see below.) However, I also get an error when I run it on bert.
It seems tkregister2 is searching for COR files, but I am using
mgz format. Am I not using the correct flags?
My subjects directory contains the talairach subject included in
the dev release. Do I need to download talairach separately?
Here is the output for subject 2335 and bert: [root@bwy-1-113mm talairach]$ tkregister2 --mgz --s 2335 --fstal INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.002 0.050 -0.017 -3.539; -0.053 1.034 -0.076 -12.275; 0.014 0.081 1.091 -14.424; 0.000 0.000 0.000 1.000; corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /freesurfer/subjects/talairach/mri/orig as
0
[root@bwy-1-113mm subjects]$ tkregister2 --mgz --s bert --fstal INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.154 -0.024 0.046 -5.813; 0.014 0.941 0.131 -21.893; -0.048 -0.155 1.123 -0.730; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /freesurfer/subjects/talairach/mri/orig as
0
[root@bwy-1-113mm subjects]$
Any help is greatly appreciated.
Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, the surface does not align with the anatomical.
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 2:20 PM >>>
So the surface does not align with the anatomical?
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
My subject's anatomical scan seems to be relatively well aligned
with
the fuzzy talairach brain, but the green 'orig' surface is
completely
off. How is this possible? Why do we need the surface at all if
it's
not used for alignment?
The tutorial advises using the 'final objective function value'
from
mritotal.log to determine if the registration is off before making
any
edits. If the registration needs to be modified, and if it's
important
to have an accurate talairach.xfm, how do I determine if it is
aligned
sufficiently after making edits?
Thanks, Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:23 PM >>>
Hit the "compare" button to flip back and forth between the
talairach
brain and your subjects anatomical.
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
How can I check the registration if I can't see the surface? -Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:07 PM >>>
If you don't have a surface, then don't run it with --surf. It's important to have an accurate talairach.xfm.
doug
On Mon, 17 Oct 2005, Sasha Wolosin wrote:
Dear Nick,
I recently installed the dev release from October 3rd, but
tkregister2 still does not work after autorecon1. (It will not load
the
orig volume because rh.orig and lh.orig do not yet exist in the surf folder for the subject) Am I not using the correct inputs for this step (my inputs are the same as that of the tutorial)? How
important
is it to have a correct registration before running autorecon2?
Here is the script for a subject who has only been run with
autorecon1:
% [root@bwy-1-113mm mri]$ tkregister2 --mgz --s 2333 --fstal
--surf
orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.538; 0.000 0.000 1.000 -132.197; 0.000 -1.000 0.000 137.708; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; subject = 2333 Reading lh surface orig MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open
file
No such file or directory tkregister2: could not read surface orig No such file or directory [root@bwy-1-113mm mri]$
If I instead run the command:tkregister2 --mgz --s 2333 --fstal tkregister2 does load, but there is no green orig outline to guide
any corrections.
If I run tkregister2 after running autorecon2, it also loads,
but
the registration is all wrong. (It was about as far off as the
tutorial
subject) Here is the output:
[root@bwy-1-113mm /freesurfer_subjects]$ tkregister2 --mgz --s
2338
--fstal --surf orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2338/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 136.359; 0.000 0.000 1.000 -135.309; -0.000 -1.000 0.000 159.346; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; subject = 2338 Reading lh surface orig Done reading surface Reading rh surface orig Done reading surface Zoom Factor = 2 FOV = 256 Opening window 2338 Setting scale tkregister2: interface: /freesurfer/lib/tcl/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change:
macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
Looking through the script I noticed it never mentions the path
to
the correct .xfm file, which is in the subjects directory (the
subjects
directory is /freesurfer_subjects, not /freesurfer/subjects) But I copied the .xfm file to the folder it was looking for, and the registration was still just as far off.
Any help is greatly appreciated, Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Nick Schmansky nicks@nmr.mgh.harvard.edu 09/15/05 2:40 PM >>>
Sasha,
An alternative solution is to create the COR files for the
talairach
subject:
cd $SUBJECTS_DIR/talairach/mri mri_convert -it mgz -ot cor orig.mgz orig/
This will deposit COR files into the orig/ directory, and your
current
tkregister2 should then work.
We are recommending using .mgz files over the older COR format,
and
are
still trying to make all the tools fully compliant.
A new 'dev' release containing the updated tkregister2 will be
posted in
the next couple days.
Nick
On Thu, 2005-09-15 at 14:26 -0400, Doug Greve wrote:
I just fixed this error. For those in the nmr center, the fix
will
be
live tomorrow. For those outside, you can download a new Linux
version
from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Sasha Wolosin wrote:
Dear all,
I am having trouble running tkregister2.
I get an error when I run tkregister2 on a subject after
running
autorecon1 (see below.) However, I also get an error when I run it
on
bert.
It seems tkregister2 is searching for COR files, but I am using
mgz format. Am I not using the correct flags?
My subjects directory contains the talairach subject included
in
the dev release. Do I need to download talairach separately?
Here is the output for subject 2335 and bert: [root@bwy-1-113mm talairach]$ tkregister2 --mgz --s 2335 --fstal INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.002 0.050 -0.017 -3.539; -0.053 1.034 -0.076 -12.275; 0.014 0.081 1.091 -14.424; 0.000 0.000 0.000 1.000; corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /freesurfer/subjects/talairach/mri/orig as
0
[root@bwy-1-113mm subjects]$ tkregister2 --mgz --s bert --fstal INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.154 -0.024 0.046 -5.813; 0.014 0.941 0.131 -21.893; -0.048 -0.155 1.123 -0.730; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /freesurfer/subjects/talairach/mri/orig as
0
[root@bwy-1-113mm subjects]$
Any help is greatly appreciated.
Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Disclaimer: The materials in this e-mail are private and may contain
Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If
you
are not the intended recipient, be advised that any unauthorized
use,
disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited.
If
you have received this e-mail in error, please immediately notify
the
sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
OK. We've replicated this problem here. I'll work on it to find out what's going on.
doug
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
yes, the surface does not align with the anatomical.
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 2:20 PM >>>
So the surface does not align with the anatomical?
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
My subject's anatomical scan seems to be relatively well aligned
with
the fuzzy talairach brain, but the green 'orig' surface is
completely
off. How is this possible? Why do we need the surface at all if
it's
not used for alignment?
The tutorial advises using the 'final objective function value'
from
mritotal.log to determine if the registration is off before making
any
edits. If the registration needs to be modified, and if it's
important
to have an accurate talairach.xfm, how do I determine if it is
aligned
sufficiently after making edits?
Thanks, Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:23 PM >>>
Hit the "compare" button to flip back and forth between the
talairach
brain and your subjects anatomical.
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
How can I check the registration if I can't see the surface? -Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:07 PM >>>
If you don't have a surface, then don't run it with --surf. It's important to have an accurate talairach.xfm.
doug
On Mon, 17 Oct 2005, Sasha Wolosin wrote:
Dear Nick,
I recently installed the dev release from October 3rd, but
tkregister2 still does not work after autorecon1. (It will not load
the
orig volume because rh.orig and lh.orig do not yet exist in the surf folder for the subject) Am I not using the correct inputs for this step (my inputs are the same as that of the tutorial)? How
important
is it to have a correct registration before running autorecon2?
Here is the script for a subject who has only been run with
autorecon1:
% [root@bwy-1-113mm mri]$ tkregister2 --mgz --s 2333 --fstal
--surf
orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.538; 0.000 0.000 1.000 -132.197; 0.000 -1.000 0.000 137.708; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; subject = 2333 Reading lh surface orig MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open
file
No such file or directory tkregister2: could not read surface orig No such file or directory [root@bwy-1-113mm mri]$
If I instead run the command:tkregister2 --mgz --s 2333 --fstal tkregister2 does load, but there is no green orig outline to guide
any corrections.
If I run tkregister2 after running autorecon2, it also loads,
but
the registration is all wrong. (It was about as far off as the
tutorial
subject) Here is the output:
[root@bwy-1-113mm /freesurfer_subjects]$ tkregister2 --mgz --s
2338
--fstal --surf orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2338/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 136.359; 0.000 0.000 1.000 -135.309; -0.000 -1.000 0.000 159.346; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; subject = 2338 Reading lh surface orig Done reading surface Reading rh surface orig Done reading surface Zoom Factor = 2 FOV = 256 Opening window 2338 Setting scale tkregister2: interface: /freesurfer/lib/tcl/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change:
macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
Looking through the script I noticed it never mentions the path
to
the correct .xfm file, which is in the subjects directory (the
subjects
directory is /freesurfer_subjects, not /freesurfer/subjects) But I copied the .xfm file to the folder it was looking for, and the registration was still just as far off.
Any help is greatly appreciated, Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
> Nick Schmansky nicks@nmr.mgh.harvard.edu 09/15/05 2:40 PM >>>
Sasha,
An alternative solution is to create the COR files for the
talairach
subject:
cd $SUBJECTS_DIR/talairach/mri mri_convert -it mgz -ot cor orig.mgz orig/
This will deposit COR files into the orig/ directory, and your
current
tkregister2 should then work.
We are recommending using .mgz files over the older COR format,
and
are
still trying to make all the tools fully compliant.
A new 'dev' release containing the updated tkregister2 will be
posted in
the next couple days.
Nick
On Thu, 2005-09-15 at 14:26 -0400, Doug Greve wrote:
I just fixed this error. For those in the nmr center, the fix
will
be
live tomorrow. For those outside, you can download a new Linux
version
from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Sasha Wolosin wrote:
Dear all,
I am having trouble running tkregister2.
I get an error when I run tkregister2 on a subject after
running
autorecon1 (see below.) However, I also get an error when I run it
on
bert.
It seems tkregister2 is searching for COR files, but I am using
mgz format. Am I not using the correct flags?
My subjects directory contains the talairach subject included
in
the dev release. Do I need to download talairach separately?
Here is the output for subject 2335 and bert: [root@bwy-1-113mm talairach]$ tkregister2 --mgz --s 2335 --fstal INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.002 0.050 -0.017 -3.539; -0.053 1.034 -0.076 -12.275; 0.014 0.081 1.091 -14.424; 0.000 0.000 0.000 1.000; corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /freesurfer/subjects/talairach/mri/orig as
0
[root@bwy-1-113mm subjects]$ tkregister2 --mgz --s bert --fstal INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.154 -0.024 0.046 -5.813; 0.014 0.941 0.131 -21.893; -0.048 -0.155 1.123 -0.730; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /freesurfer/subjects/talairach/mri/orig as
0
[root@bwy-1-113mm subjects]$
Any help is greatly appreciated.
Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Disclaimer: The materials in this e-mail are private and may contain
Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If
you
are not the intended recipient, be advised that any unauthorized
use,
disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited.
If
you have received this e-mail in error, please immediately notify
the
sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
In the meantime, is there any benefit to processing brains, or would most of the reconstruction steps need to be re-run after this problem is fixed? How much of the reconstruction needs to be re-run after manually fixing a bad talairach.xfm? Thanks, Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 8:08 PM >>>
OK. We've replicated this problem here. I'll work on it to find out what's going on.
doug
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
yes, the surface does not align with the anatomical.
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 2:20 PM >>>
So the surface does not align with the anatomical?
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
My subject's anatomical scan seems to be relatively well aligned
with
the fuzzy talairach brain, but the green 'orig' surface is
completely
off. How is this possible? Why do we need the surface at all if
it's
not used for alignment?
The tutorial advises using the 'final objective function value'
from
mritotal.log to determine if the registration is off before making
any
edits. If the registration needs to be modified, and if it's
important
to have an accurate talairach.xfm, how do I determine if it is
aligned
sufficiently after making edits?
Thanks, Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:23 PM >>>
Hit the "compare" button to flip back and forth between the
talairach
brain and your subjects anatomical.
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
How can I check the registration if I can't see the surface? -Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:07 PM >>>
If you don't have a surface, then don't run it with --surf. It's important to have an accurate talairach.xfm.
doug
On Mon, 17 Oct 2005, Sasha Wolosin wrote:
Dear Nick,
I recently installed the dev release from October 3rd, but
tkregister2 still does not work after autorecon1. (It will not
load
the
orig volume because rh.orig and lh.orig do not yet exist in the
surf
folder for the subject) Am I not using the correct inputs for
this
step (my inputs are the same as that of the tutorial)? How
important
is it to have a correct registration before running autorecon2?
Here is the script for a subject who has only been run with
autorecon1:
% [root@bwy-1-113mm mri]$ tkregister2 --mgz --s 2333 --fstal
--surf
orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.538; 0.000 0.000 1.000 -132.197; 0.000 -1.000 0.000 137.708; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; subject = 2333 Reading lh surface orig MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open
file
No such file or directory tkregister2: could not read surface orig No such file or directory [root@bwy-1-113mm mri]$
If I instead run the command:tkregister2 --mgz --s 2333 --fstal tkregister2 does load, but there is no green orig outline to
guide
any corrections.
If I run tkregister2 after running autorecon2, it also loads,
but
the registration is all wrong. (It was about as far off as the
tutorial
subject) Here is the output:
[root@bwy-1-113mm /freesurfer_subjects]$ tkregister2 --mgz --s
2338
--fstal --surf orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2338/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 136.359; 0.000 0.000 1.000 -135.309; -0.000 -1.000 0.000 159.346; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; subject = 2338 Reading lh surface orig Done reading surface Reading rh surface orig Done reading surface Zoom Factor = 2 FOV = 256 Opening window 2338 Setting scale tkregister2: interface: /freesurfer/lib/tcl/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change:
macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
Looking through the script I noticed it never mentions the path
to
the correct .xfm file, which is in the subjects directory (the
subjects
directory is /freesurfer_subjects, not /freesurfer/subjects) But I copied the .xfm file to the folder it was looking for, and the registration was still just as far off.
Any help is greatly appreciated, Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
> Nick Schmansky nicks@nmr.mgh.harvard.edu 09/15/05 2:40 PM
Sasha,
An alternative solution is to create the COR files for the
talairach
subject:
cd $SUBJECTS_DIR/talairach/mri mri_convert -it mgz -ot cor orig.mgz orig/
This will deposit COR files into the orig/ directory, and your
current
tkregister2 should then work.
We are recommending using .mgz files over the older COR format,
and
are
still trying to make all the tools fully compliant.
A new 'dev' release containing the updated tkregister2 will be
posted in
the next couple days.
Nick
On Thu, 2005-09-15 at 14:26 -0400, Doug Greve wrote:
I just fixed this error. For those in the nmr center, the fix
will
be
live tomorrow. For those outside, you can download a new Linux
version
from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Sasha Wolosin wrote:
Dear all,
I am having trouble running tkregister2.
I get an error when I run tkregister2 on a subject after
running
autorecon1 (see below.) However, I also get an error when I run it
on
bert.
It seems tkregister2 is searching for COR files, but I am
using
mgz format. Am I not using the correct flags?
My subjects directory contains the talairach subject included
in
the dev release. Do I need to download talairach separately?
Here is the output for subject 2335 and bert: [root@bwy-1-113mm talairach]$ tkregister2 --mgz --s 2335
--fstal
INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.002 0.050 -0.017 -3.539; -0.053 1.034 -0.076 -12.275; 0.014 0.081 1.091 -14.424; 0.000 0.000 0.000 1.000; corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /freesurfer/subjects/talairach/mri/orig
as
0
[root@bwy-1-113mm subjects]$ tkregister2 --mgz --s bert --fstal INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.154 -0.024 0.046 -5.813; 0.014 0.941 0.131 -21.893; -0.048 -0.155 1.123 -0.730; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /freesurfer/subjects/talairach/mri/orig
as
0
[root@bwy-1-113mm subjects]$
Any help is greatly appreciated.
Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Disclaimer: The materials in this e-mail are private and may contain
Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations.
If
you
are not the intended recipient, be advised that any unauthorized
use,
disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly
prohibited.
If
you have received this e-mail in error, please immediately notify
the
sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I've tracked down and fixed the problem. It will be live in the NMR center tomorrow, but I don't know the best way to get a fix to you. This does not actually affect your talairach registration, it was just a problem displaying the surfaces. If you flip bet the talairach and the anat, and they look aligned, then you can continue with the analysis.
doug
On Wed, 19 Oct 2005, Sasha Wolosin wrote:
In the meantime, is there any benefit to processing brains, or would most of the reconstruction steps need to be re-run after this problem is fixed? How much of the reconstruction needs to be re-run after manually fixing a bad talairach.xfm? Thanks, Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 8:08 PM >>>
OK. We've replicated this problem here. I'll work on it to find out what's going on.
doug
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
yes, the surface does not align with the anatomical.
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 2:20 PM >>>
So the surface does not align with the anatomical?
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
My subject's anatomical scan seems to be relatively well aligned
with
the fuzzy talairach brain, but the green 'orig' surface is
completely
off. How is this possible? Why do we need the surface at all if
it's
not used for alignment?
The tutorial advises using the 'final objective function value'
from
mritotal.log to determine if the registration is off before making
any
edits. If the registration needs to be modified, and if it's
important
to have an accurate talairach.xfm, how do I determine if it is
aligned
sufficiently after making edits?
Thanks, Sasha
Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:23 PM >>>
Hit the "compare" button to flip back and forth between the
talairach
brain and your subjects anatomical.
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
How can I check the registration if I can't see the surface? -Sasha
> Doug Greve greve@nmr.mgh.harvard.edu 10/18/2005 12:07 PM >>>
If you don't have a surface, then don't run it with --surf. It's important to have an accurate talairach.xfm.
doug
On Mon, 17 Oct 2005, Sasha Wolosin wrote:
Dear Nick,
I recently installed the dev release from October 3rd, but
tkregister2 still does not work after autorecon1. (It will not
load
the
orig volume because rh.orig and lh.orig do not yet exist in the
surf
folder for the subject) Am I not using the correct inputs for
this
step (my inputs are the same as that of the tutorial)? How
important
is it to have a correct registration before running autorecon2?
Here is the script for a subject who has only been run with
autorecon1:
% [root@bwy-1-113mm mri]$ tkregister2 --mgz --s 2333 --fstal
--surf
orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.538; 0.000 0.000 1.000 -132.197; 0.000 -1.000 0.000 137.708; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; subject = 2333 Reading lh surface orig MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open
file
No such file or directory tkregister2: could not read surface orig No such file or directory [root@bwy-1-113mm mri]$
If I instead run the command:tkregister2 --mgz --s 2333 --fstal tkregister2 does load, but there is no green orig outline to
guide
any corrections.
If I run tkregister2 after running autorecon2, it also loads,
but
the registration is all wrong. (It was about as far off as the
tutorial
subject) Here is the output:
[root@bwy-1-113mm /freesurfer_subjects]$ tkregister2 --mgz --s
2338
--fstal --surf orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig
volume.
target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2338/mri/orig.mgz WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 136.359; 0.000 0.000 1.000 -135.309; -0.000 -1.000 0.000 159.346; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz INFO: changing move type to float Tmov: -------------------- -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; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; subject = 2338 Reading lh surface orig Done reading surface Reading rh surface orig Done reading surface Zoom Factor = 2 FOV = 256 Opening window 2338 Setting scale tkregister2: interface: /freesurfer/lib/tcl/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change:
macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
Looking through the script I noticed it never mentions the path
to
the correct .xfm file, which is in the subjects directory (the
subjects
directory is /freesurfer_subjects, not /freesurfer/subjects) But I copied the .xfm file to the folder it was looking for, and the registration was still just as far off.
Any help is greatly appreciated, Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
>> Nick Schmansky nicks@nmr.mgh.harvard.edu 09/15/05 2:40 PM
Sasha,
An alternative solution is to create the COR files for the
talairach
subject:
cd $SUBJECTS_DIR/talairach/mri mri_convert -it mgz -ot cor orig.mgz orig/
This will deposit COR files into the orig/ directory, and your
current
tkregister2 should then work.
We are recommending using .mgz files over the older COR format,
and
are
still trying to make all the tools fully compliant.
A new 'dev' release containing the updated tkregister2 will be
posted in
the next couple days.
Nick
On Thu, 2005-09-15 at 14:26 -0400, Doug Greve wrote:
I just fixed this error. For those in the nmr center, the fix
will
be
live tomorrow. For those outside, you can download a new Linux
version
from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Sasha Wolosin wrote:
> Dear all, > > I am having trouble running tkregister2. > > I get an error when I run tkregister2 on a subject after
running
autorecon1 (see below.) However, I also get an error when I run it
on
bert.
> It seems tkregister2 is searching for COR files, but I am
using
mgz format. Am I not using the correct flags?
> > My subjects directory contains the talairach subject included
in
the dev release. Do I need to download talairach separately?
> > Here is the output for subject 2335 and bert: > [root@bwy-1-113mm talairach]$ tkregister2 --mgz --s 2335
--fstal
> INFO: no target volume specified, assuming FreeSurfer orig
volume.
> target volume orig > movable volume (null) > reg file (null) > LoadVol 1 > $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ > Diagnostic Level -1 > talairach.xfm --------------------- > 1.002 0.050 -0.017 -3.539; > -0.053 1.034 -0.076 -12.275; > 0.014 0.081 1.091 -14.424; > 0.000 0.000 0.000 1.000; > corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
> ERROR: could not read /freesurfer/subjects/talairach/mri/orig
as
0
> > > [root@bwy-1-113mm subjects]$ tkregister2 --mgz --s bert --fstal > INFO: no target volume specified, assuming FreeSurfer orig
volume.
> target volume orig > movable volume (null) > reg file (null) > LoadVol 1 > $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ > Diagnostic Level -1 > talairach.xfm --------------------- > 1.154 -0.024 0.046 -5.813; > 0.014 0.941 0.131 -21.893; > -0.048 -0.155 1.123 -0.730; > 0.000 0.000 0.000 1.000; > WARNING: can't find the talairach xform
'/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm'
> WARNING: transform is not loaded into mri > corRead(): can't open file
/freesurfer/subjects/talairach/mri/orig/COR-.info
> ERROR: could not read /freesurfer/subjects/talairach/mri/orig
as
0
> [root@bwy-1-113mm subjects]$ > > > Any help is greatly appreciated. > > Thanks, > Sasha > > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 > wolosin@kennedykrieger.org > > > > Disclaimer: > The materials in this e-mail are private and may contain
Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations.
If
you
are not the intended recipient, be advised that any unauthorized
use,
disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly
prohibited.
If
you have received this e-mail in error, please immediately notify
the
sender via telephone or return e-mail.
> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Nick Schmansky -
Sasha Wolosin