Hi, I am using the command to check my registration and getting this error message: could not find orig as either mgz or COR. This is the command I am using. tkregister2 --mov 18135.RS.mgz --reg 18135_RS_register.dat --surf ----------------------------------------OUTPUT-------------------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume 18135.RS.mgz reg file 18135_RS_register.dat LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.994 -0.040 0.100 2.799; -0.097 -0.071 -0.993 2.262; -0.047 0.997 -0.067 5.775; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- ERROR: could not find orig as either mgz or COR ------------------------------------------------------------------------------------------------
what is your SUBJECTS_DIR env variable? On Tue, 18 Dec 2012, priyank wrote:
Hi, I am using the command to check my registration and getting this error message: could not find orig as either mgz or COR. This is the command I am using. tkregister2 --mov 18135.RS.mgz --reg 18135_RS_register.dat --surf ----------------------------------------OUTPUT-------------------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume 18135.RS.mgz reg file 18135_RS_register.dat LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.994 -0.040 0.100 2.799; -0.097 -0.071 -0.993 2.262; -0.047 0.997 -0.067 5.775; 0.000 0.000 0.000 1.000; float2int = 0
ERROR: could not find orig as either mgz or COR
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I have these files in the folder 18135. 18135.RS.mgz 18135_RS_register.dat.log 18135_RS_register.dat.sum 18135.RS+orig.BRIK 18135_RS_register.dat.log.old 18135.RS.template.mgz 18135.RS+orig.HEAD 18135_RS_register.dat.mincost 18135_RS_register.dat 18135_RS_register.dat.param
and other freesurfer files in the folder 18135_FS (in the respective folders.. mri, surf...)...
I copied 18135.RS.mgz in the 18135_FS/mri/orig folder also.
I have tried both directories to be SUBJECTS_DIR but it didn't work.
Do I need to move all the files in 18135_FS/mri/orig folder?
On 12/18/2012 4:38 PM, Bruce Fischl wrote:
what is your SUBJECTS_DIR env variable? On Tue, 18 Dec 2012, priyank wrote:
Hi, I am using the command to check my registration and getting this error message: could not find orig as either mgz or COR. This is the command I am using. tkregister2 --mov 18135.RS.mgz --reg 18135_RS_register.dat --surf ----------------------------------------OUTPUT--------------------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume 18135.RS.mgz reg file 18135_RS_register.dat LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.994 -0.040 0.100 2.799; -0.097 -0.071 -0.993 2.262; -0.047 0.997 -0.067 5.775; 0.000 0.000 0.000 1.000; float2int = 0
ERROR: could not find orig as either mgz or COR
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you don't need to move them. Where is the subject data that you ran recon-all on? You need to setenv SUBJECTS_DIR to point to that directory (the one that contains the subject you reconned)
cheers Bruce
On Tue, 18 Dec 2012, priyank wrote:
I have these files in the folder 18135. 18135.RS.mgz 18135_RS_register.dat.log 18135_RS_register.dat.sum 18135.RS+orig.BRIK 18135_RS_register.dat.log.old 18135.RS.template.mgz 18135.RS+orig.HEAD 18135_RS_register.dat.mincost 18135_RS_register.dat 18135_RS_register.dat.param
and other freesurfer files in the folder 18135_FS (in the respective folders.. mri, surf...)...
I copied 18135.RS.mgz in the 18135_FS/mri/orig folder also.
I have tried both directories to be SUBJECTS_DIR but it didn't work.
Do I need to move all the files in 18135_FS/mri/orig folder?
On 12/18/2012 4:38 PM, Bruce Fischl wrote: what is your SUBJECTS_DIR env variable? On Tue, 18 Dec 2012, priyank wrote:
Hi, I am using the command to check my registration and getting this error message: could not find orig as either mgz or COR. This is the command I am using. tkregister2 --mov 18135.RS.mgz --reg 18135_RS_register.dat --surf----------------------------------------OUTPUT-----------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume 18135.RS.mgz reg file 18135_RS_register.dat LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.994 -0.040 0.100 2.799; -0.097 -0.071 -0.993 2.262; -0.047 0.997 -0.067 5.775; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- ERROR: could not find orig as either mgz or COR
--------------------- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Actually I received the reconned data. I did bbregistration: bbregister --s ${sub}_FS --mov $main_path/$sub/${sub}.RS.mgz --reg ${sub}_RS_register.dat --init-fsl --bold --frame $framenum --nearest --o ${sub}.RS.template.mgz
where $sub is subject id, which is 18135.
And now all the files are in 18135_FS. I only have resting state file in separate folder (18135).
On 12/18/2012 5:16 PM, Bruce Fischl wrote:
you don't need to move them. Where is the subject data that you ran recon-all on? You need to setenv SUBJECTS_DIR to point to that directory (the one that contains the subject you reconned)
cheers Bruce
On Tue, 18 Dec 2012, priyank wrote:
I have these files in the folder 18135. 18135.RS.mgz 18135_RS_register.dat.log 18135_RS_register.dat.sum 18135.RS+orig.BRIK 18135_RS_register.dat.log.old 18135.RS.template.mgz 18135.RS+orig.HEAD 18135_RS_register.dat.mincost 18135_RS_register.dat 18135_RS_register.dat.param
and other freesurfer files in the folder 18135_FS (in the respective folders.. mri, surf...)...
I copied 18135.RS.mgz in the 18135_FS/mri/orig folder also.
I have tried both directories to be SUBJECTS_DIR but it didn't work.
Do I need to move all the files in 18135_FS/mri/orig folder?
On 12/18/2012 4:38 PM, Bruce Fischl wrote: what is your SUBJECTS_DIR env variable? On Tue, 18 Dec 2012, priyank wrote:
Hi, I am using the command to check my registration and getting this error message: could not find orig as either mgz or COR. This is the command I am using. tkregister2 --mov 18135.RS.mgz --reg 18135_RS_register.dat --surf----------------------------------------OUTPUT-----------------------------
--------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume 18135.RS.mgz reg file 18135_RS_register.dat LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.994 -0.040 0.100 2.799; -0.097 -0.071 -0.993 2.262; -0.047 0.997 -0.067 5.775; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- ERROR: could not find orig as either mgz or COR
--------------------- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Is $SUBJECTS_DIR/$subject exist?
On 12/18/2012 05:13 PM, priyank wrote:
I have these files in the folder 18135. 18135.RS.mgz 18135_RS_register.dat.log 18135_RS_register.dat.sum 18135.RS+orig.BRIK 18135_RS_register.dat.log.old 18135.RS.template.mgz 18135.RS+orig.HEAD 18135_RS_register.dat.mincost 18135_RS_register.dat 18135_RS_register.dat.param
and other freesurfer files in the folder 18135_FS (in the respective folders.. mri, surf...)...
I copied 18135.RS.mgz in the 18135_FS/mri/orig folder also.
I have tried both directories to be SUBJECTS_DIR but it didn't work.
Do I need to move all the files in 18135_FS/mri/orig folder?
On 12/18/2012 4:38 PM, Bruce Fischl wrote:
what is your SUBJECTS_DIR env variable? On Tue, 18 Dec 2012, priyank wrote:
Hi, I am using the command to check my registration and getting this error message: could not find orig as either mgz or COR. This is the command I am using. tkregister2 --mov 18135.RS.mgz --reg 18135_RS_register.dat --surf ----------------------------------------OUTPUT--------------------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume 18135.RS.mgz reg file 18135_RS_register.dat LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.994 -0.040 0.100 2.799; -0.097 -0.071 -0.993 2.262; -0.047 0.997 -0.067 5.775; 0.000 0.000 0.000 1.000; float2int = 0
ERROR: could not find orig as either mgz or COR
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
priyank