Dear freesurfer-mailinglist,
I'm struggling since a few days with a problem I can't resolve: I ran recon-all without errors on my data and got the surfaces. Now I want to display surf/l(r)h.pial and mri/T1.mgz (or /orig/001.mgz) together to check the result in slicer3 (3.61.0). The problem occurring is, that any surface and the original volumes do not fit together - there is a small shift of the surfaces to the front. I already tried to apply transforms from mri/transform to the T1.mgz but nothing solved that issue.
here is a screen shot of my problem: http://dl.dropbox.com/u/1263357/problem.png
What am I doing wrong?
Thank you for any hint in advance Best Regards Steffen
Hi Steffen,
presumably this problem does not occur in tkmedit or freeview? If not, then you probably should contact the slicer folks and ask them. It's almost certainly caused by a nonzero c_ras in your data (you can run mri_info on the orig.mgz, or mris_info on the ?h.pial to check that this is true).
cheers, Bruce
On Fri, 16 Jul 2010, Steffen Bollmann wrote:
Dear freesurfer-mailinglist,
I'm struggling since a few days with a problem I can't resolve: I ran recon-all without errors on my data and got the surfaces. Now I want to display surf/l(r)h.pial and mri/T1.mgz (or /orig/001.mgz) together to check the result in slicer3 (3.61.0). The problem occurring is, that any surface and the original volumes do not fit together - there is a small shift of the surfaces to the front. I already tried to apply transforms from mri/transform to the T1.mgz but nothing solved that issue.
here is a screen shot of my problem: http://dl.dropbox.com/u/1263357/problem.png
What am I doing wrong?
Thank you for any hint in advance Best Regards Steffen
Thank you so much for your quick response :)
presumably this problem does not occur in tkmedit or freeview?
it works fine in tkmedit, but in freeview the same (or similar?) problem occurred: (volume: orig.mgz (http://dl.dropbox.com/u/1263357/orig.mgz) ; surface: rh.pial (http://dl.dropbox.com/u/1263357/rh.pial)) screenshot: http://dl.dropbox.com/u/1263357/cras_problem_freeview.png
It's almost certainly caused by a nonzero c_ras in your data (you can run mri_info on the orig.mgz, or mris_info on the ?h.pial to check that this is true).
you are right: the c_ras is non zero in orig.mgz: -2.57772 14.6127 -8.48792
Is there a way to correct that cras -value? (I need to to further processing in a small and unknown software, which is based on VTK and this shows the same issue - might this even be a problem in the VTK-framework?)
Thank you Steffen
cheers, Bruce
On Fri, 16 Jul 2010, Steffen Bollmann wrote:
Dear freesurfer-mailinglist,
I'm struggling since a few days with a problem I can't resolve: I ran recon-all without errors on my data and got the surfaces. Now I want to display surf/l(r)h.pial and mri/T1.mgz (or /orig/001.mgz) together to check the result in slicer3 (3.61.0). The problem occurring is, that any surface and the original volumes do not fit together - there is a small shift of the surfaces to the front. I already tried to apply transforms from mri/transform to the T1.mgz but nothing solved that issue.
here is a screen shot of my problem: http://dl.dropbox.com/u/1263357/problem.png
What am I doing wrong?
Thank you for any hint in advance Best Regards Steffen
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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.
you don't have to correct it. Slicer needs to be able to read it from the volumes and surfaces to properly display them. On Sat, 17 Jul 2010, Steffen Bollmann wrote:
Thank you so much for your quick response :)
presumably this problem does not occur in tkmedit or freeview?
it works fine in tkmedit, but in freeview the same (or similar?) problem occurred: (volume: orig.mgz (http://dl.dropbox.com/u/1263357/orig.mgz) ; surface: rh.pial (http://dl.dropbox.com/u/1263357/rh.pial)) screenshot: http://dl.dropbox.com/u/1263357/cras_problem_freeview.png
It's almost certainly caused by a nonzero c_ras in your data (you can run mri_info on the orig.mgz, or mris_info on the ?h.pial to check that this is true).
you are right: the c_ras is non zero in orig.mgz: -2.57772 14.6127 -8.48792
Is there a way to correct that cras -value? (I need to to further processing in a small and unknown software, which is based on VTK and this shows the same issue - might this even be a problem in the VTK-framework?)
Thank you Steffen
cheers, Bruce
On Fri, 16 Jul 2010, Steffen Bollmann wrote:
Dear freesurfer-mailinglist,
I'm struggling since a few days with a problem I can't resolve: I ran recon-all without errors on my data and got the surfaces. Now I want to display surf/l(r)h.pial and mri/T1.mgz (or /orig/001.mgz) together to check the result in slicer3 (3.61.0). The problem occurring is, that any surface and the original volumes do not fit together - there is a small shift of the surfaces to the front. I already tried to apply transforms from mri/transform to the T1.mgz but nothing solved that issue.
here is a screen shot of my problem: http://dl.dropbox.com/u/1263357/problem.png
What am I doing wrong?
Thank you for any hint in advance Best Regards Steffen
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
In freeview if you load the volume first before loading the surface, they should align.
Ruopeng
On 7/17/10 5:26 AM, Steffen Bollmann wrote:
Thank you so much for your quick response :)
presumably this problem does not occur in tkmedit or freeview?
it works fine in tkmedit, but in freeview the same (or similar?) problem occurred: (volume: orig.mgz (http://dl.dropbox.com/u/1263357/orig.mgz) ; surface: rh.pial (http://dl.dropbox.com/u/1263357/rh.pial)) screenshot: http://dl.dropbox.com/u/1263357/cras_problem_freeview.png
It's almost certainly caused by a nonzero c_ras in your data (you can run mri_info on the orig.mgz, or mris_info on the ?h.pial to check that this is true).
you are right: the c_ras is non zero in orig.mgz: -2.57772 14.6127 -8.48792
Is there a way to correct that cras -value? (I need to to further processing in a small and unknown software, which is based on VTK and this shows the same issue - might this even be a problem in the VTK-framework?)
Thank you Steffen
cheers, Bruce
On Fri, 16 Jul 2010, Steffen Bollmann wrote:
Dear freesurfer-mailinglist,
I'm struggling since a few days with a problem I can't resolve: I ran recon-all without errors on my data and got the surfaces. Now I want to display surf/l(r)h.pial and mri/T1.mgz (or /orig/001.mgz) together to check the result in slicer3 (3.61.0). The problem occurring is, that any surface and the original volumes do not fit together - there is a small shift of the surfaces to the front. I already tried to apply transforms from mri/transform to the T1.mgz but nothing solved that issue.
here is a screen shot of my problem: http://dl.dropbox.com/u/1263357/problem.png
What am I doing wrong?
Thank you for any hint in advance Best Regards Steffen
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
Am 18.07.2010 06:08, schrieb Ruopeng Wang:
In freeview if you load the volume first before loading the surface, they should align.
I tried it in this order - result: It is still not working :( these are the files I tried: volume: http://dl.dropbox.com/u/1263357/orig.mgz surface: http://dl.dropbox.com/u/1263357/rh.pial
the version of freeview I used: 1.0 (internal) build Aug 11 2009
Is it possible to calculate a transformation based on that possibly wrong c_ras-value to get a corrected image with zero c_ras, so all programs ignoring that value don't have a problem :?
Thank you for your help Steffen
Ruopeng
On 7/17/10 5:26 AM, Steffen Bollmann wrote:
Thank you so much for your quick response :)
presumably this problem does not occur in tkmedit or freeview?
it works fine in tkmedit, but in freeview the same (or similar?) problem occurred: (volume: orig.mgz (http://dl.dropbox.com/u/1263357/orig.mgz) ; surface: rh.pial (http://dl.dropbox.com/u/1263357/rh.pial)) screenshot: http://dl.dropbox.com/u/1263357/cras_problem_freeview.png
It's almost certainly caused by a nonzero c_ras in your data (you can run mri_info on the orig.mgz, or mris_info on the ?h.pial to check that this is true).
you are right: the c_ras is non zero in orig.mgz: -2.57772 14.6127 -8.48792
Is there a way to correct that cras -value? (I need to to further processing in a small and unknown software, which is based on VTK and this shows the same issue - might this even be a problem in the VTK-framework?)
Thank you Steffen
cheers, Bruce
On Fri, 16 Jul 2010, Steffen Bollmann wrote:
Dear freesurfer-mailinglist,
I'm struggling since a few days with a problem I can't resolve: I ran recon-all without errors on my data and got the surfaces. Now I want to display surf/l(r)h.pial and mri/T1.mgz (or /orig/001.mgz) together to check the result in slicer3 (3.61.0). The problem occurring is, that any surface and the original volumes do not fit together - there is a small shift of the surfaces to the front. I already tried to apply transforms from mri/transform to the T1.mgz but nothing solved that issue.
here is a screen shot of my problem: http://dl.dropbox.com/u/1263357/problem.png
What am I doing wrong?
Thank you for any hint in advance Best Regards Steffen
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
-
Bruce Fischl -
Ruopeng Wang -
Steffen Bollmann