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:
% [EMAIL PROTECTED] 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
[EMAIL PROTECTED] 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:
[EMAIL PROTECTED] /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
[EMAIL PROTECTED]
Nick Schmansky <[EMAIL PROTECTED]> 09/15/05 2:40 PM >>>
Sasha,
An alternative solution is to create the COR files for the talairach
subject:
cd $SUBJECTS_DIR/talairach/mri
mri_convert -it mgz -ot cor orig.mgz orig/
This will deposit COR files into the orig/ directory, and your current
tkregister2 should then work.
We are recommending using .mgz files over the older COR format, and are
still trying to make all the tools fully compliant.
A new 'dev' release containing the updated tkregister2 will be posted in
the next couple days.
Nick
On Thu, 2005-09-15 at 14:26 -0400, Doug Greve wrote:
I just fixed this error. For those in the nmr center, the fix will be
live tomorrow. For those outside, you can download a new Linux version
from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Sasha Wolosin wrote:
Dear all,
I am having trouble running tkregister2.
I get an error when I run tkregister2 on a subject after running autorecon1
(see below.) However, I also get an error when I run it on bert.
It seems tkregister2 is searching for COR files, but I am using mgz format.
Am I not using the correct flags?
My subjects directory contains the talairach subject included in the dev
release. Do I need to download talairach separately?
Here is the output for subject 2335 and bert:
[EMAIL PROTECTED] talairach]$ 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
[EMAIL PROTECTED] 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
[EMAIL PROTECTED] 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
[EMAIL PROTECTED]
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--
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MGH-NMR Center
[EMAIL PROTECTED]
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