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
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 -
Sasha Wolosin