Dear Paul,
I think that the transform window in freeview opens by default to enable manual refinement of registration if needed.
If you are not sure, try also tkregister2. It should work to simply replace tkregisterfv by tkregister2, the command would be
tkregister2 --mov your_moveable --targ your_target --reg your_lta
or, if you registered your PET to freesurfer-processed subject and want also to display surfaces, you should use tkregister2, no tkregisterfv (according to the freeview warning). The command in this case would be
tkregister2 --mov your_moveable --s your_subject_id --reg your_lta --surfs
Antonin
Hello Antonin, Thank you for your quick reply. Does this mean I should close the transform window when it opens? The alignment looks good to me, I was worried because the transform window opened and the info on the terminal window. I haven't used tkregister2 before. Do I replace tkregisterfv with tkregister2 like this " tkregister2 --mov template.nii.gz --reg template.reg.lta --surfs"? Thanks. Best, Paul Sent from my BlackBerry 10 smartphone.
From: Antonin Skoch Sent: Sunday, February 26, 2017 3:50 PM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] Fw: PETsurfer mri_coreg problem Dear Paul,
LTA means transformation matrix stored in .lta format.
This matrix can encode transformation between various coordinate spaces.
What coordinate systems transform this .lta from and to is specified by string in the .lta file. Typically this type could be vox2RAS, RAS2vox, vox2vox or RAS2RAS. Most typically the type is vox2vox.
The explanation of coordinate systems is specified for example here: http://freesurfer.net/fswiki/CoordinateSystems http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm
The output of freeview is only info, not error, indicating that your .lta is not of type vox2vox. I personally still use tkregister2 for checking of registration, since the freeview does not contain full functionality for checking transformations (see the warning). Therefore I have no experience with tkregisterfv and consider tkregister2 still as a "gold standard". However, if you use tkregisterfv for checkning transformation between volumes and the output is only "info", I would guess that everything is OK and you do not need to be bothered.
Btw, does the alignment of the images seem reasonable? How does it look in tkregister2?
Regards,
Antonin
Hello Antonin and Doug,
I viewed it in tkregister2 and I think the co-registration worked. Is there a way to extract info from both PET and anatomical to confirm the co-registration? Best, Paul
On Sun, Feb 26, 2017 at 4:49 PM, Antonin Skoch ansk@ikem.cz wrote:
Dear Paul,
I think that the transform window in freeview opens by default to enable manual refinement of registration if needed.
If you are not sure, try also tkregister2. It should work to simply replace tkregisterfv by tkregister2, the command would be
tkregister2 --mov your_moveable --targ your_target --reg your_lta
or, if you registered your PET to freesurfer-processed subject and want also to display surfaces, you should use tkregister2, no tkregisterfv (according to the freeview warning). The command in this case would be
tkregister2 --mov your_moveable --s your_subject_id --reg your_lta --surfs
Antonin
Hello Antonin, Thank you for your quick reply. Does this mean I should close the transform window when it opens? The alignment looks good to me, I was worried because the transform window opened and the info on the terminal window. I haven't used tkregister2 before. Do I replace tkregisterfv with tkregister2 like this " tkregister2 --mov template.nii.gz --reg template.reg.lta --surfs"? Thanks. Best, Paul Sent from my BlackBerry 10 smartphone. *From: *Antonin Skoch *Sent: *Sunday, February 26, 2017 3:50 PM *To: *freesurfer@nmr.mgh.harvard.edu *Reply To: *Freesurfer support list *Subject: *Re: [Freesurfer] Fw: PETsurfer mri_coreg problem
Dear Paul,
LTA means transformation matrix stored in .lta format.
This matrix can encode transformation between various coordinate spaces.
What coordinate systems transform this .lta from and to is specified by string in the .lta file. Typically this type could be vox2RAS, RAS2vox, vox2vox or RAS2RAS. Most typically the type is vox2vox.
The explanation of coordinate systems is specified for example here: http://freesurfer.net/fswiki/CoordinateSystems http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm
The output of freeview is only info, not error, indicating that your .lta is not of type vox2vox. I personally still use tkregister2 for checking of registration, since the freeview does not contain full functionality for checking transformations (see the warning). Therefore I have no experience with tkregisterfv and consider tkregister2 still as a "gold standard". However, if you use tkregisterfv for checkning transformation between volumes and the output is only "info", I would guess that everything is OK and you do not need to be bothered.
Btw, does the alignment of the images seem reasonable? How does it look in tkregister2?
Regards,
Antonin
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.
I'm not sure what you mean. If the registration looks good, what do you need to extract?
On 2/27/17 9:03 AM, miracle ozzoude wrote:
Hello Antonin and Doug,
I viewed it in tkregister2 and I think the co-registration worked. Is there a way to extract info from both PET and anatomical to confirm the co-registration? Best, Paul
On Sun, Feb 26, 2017 at 4:49 PM, Antonin Skoch <ansk@ikem.cz mailto:ansk@ikem.cz> wrote:
Dear Paul, I think that the transform window in freeview opens by default to enable manual refinement of registration if needed. If you are not sure, try also tkregister2. It should work to simply replace tkregisterfv by tkregister2, the command would be tkregister2 --mov your_moveable --targ your_target --reg your_lta or, if you registered your PET to freesurfer-processed subject and want also to display surfaces, you should use tkregister2, no tkregisterfv (according to the freeview warning). The command in this case would be tkregister2 --mov your_moveable --s your_subject_id --reg your_lta --surfs Antonin Hello Antonin, Thank you for your quick reply. Does this mean I should close the transform window when it opens? The alignment looks good to me, I was worried because the transform window opened and the info on the terminal window. I haven't used tkregister2 before. Do I replace tkregisterfv with tkregister2 like this " tkregister2 --mov template.nii.gz --reg template.reg.lta --surfs"? Thanks. Best, Paul Sent from my BlackBerry 10 smartphone. *From: *Antonin Skoch *Sent: *Sunday, February 26, 2017 3:50 PM *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Reply To: *Freesurfer support list *Subject: *Re: [Freesurfer] Fw: PETsurfer mri_coreg problem Dear Paul, LTA means transformation matrix stored in .lta format. This matrix can encode transformation between various coordinate spaces. What coordinate systems transform this .lta from and to is specified by string in the .lta file. Typically this type could be vox2RAS, RAS2vox, vox2vox or RAS2RAS. Most typically the type is vox2vox. The explanation of coordinate systems is specified for example here: http://freesurfer.net/fswiki/CoordinateSystems <http://freesurfer.net/fswiki/CoordinateSystems> http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm <http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm> The output of freeview is only info, not error, indicating that your .lta is not of type vox2vox. I personally still use tkregister2 for checking of registration, since the freeview does not contain full functionality for checking transformations (see the warning). Therefore I have no experience with tkregisterfv and consider tkregister2 still as a "gold standard". However, if you use tkregisterfv for checkning transformation between volumes and the output is only "info", I would guess that everything is OK and you do not need to be bothered. Btw, does the alignment of the images seem reasonable? How does it look in tkregister2? Regards, Antonin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
Hello Doug, Thanks for replying. I meant like coordinate points on both images to compare (i.e., any metric different from visual inspection). Best, Paul.
On Mon, Feb 27, 2017 at 10:50 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
I'm not sure what you mean. If the registration looks good, what do you need to extract?
On 2/27/17 9:03 AM, miracle ozzoude wrote:
Hello Antonin and Doug,
I viewed it in tkregister2 and I think the co-registration worked. Is there a way to extract info from both PET and anatomical to confirm the co-registration? Best, Paul
On Sun, Feb 26, 2017 at 4:49 PM, Antonin Skoch ansk@ikem.cz wrote:
Dear Paul,
I think that the transform window in freeview opens by default to enable manual refinement of registration if needed.
If you are not sure, try also tkregister2. It should work to simply replace tkregisterfv by tkregister2, the command would be
tkregister2 --mov your_moveable --targ your_target --reg your_lta
or, if you registered your PET to freesurfer-processed subject and want also to display surfaces, you should use tkregister2, no tkregisterfv (according to the freeview warning). The command in this case would be
tkregister2 --mov your_moveable --s your_subject_id --reg your_lta --surfs
Antonin
Hello Antonin, Thank you for your quick reply. Does this mean I should close the transform window when it opens? The alignment looks good to me, I was worried because the transform window opened and the info on the terminal window. I haven't used tkregister2 before. Do I replace tkregisterfv with tkregister2 like this " tkregister2 --mov template.nii.gz --reg template.reg.lta --surfs"? Thanks. Best, Paul Sent from my BlackBerry 10 smartphone. *From: *Antonin Skoch *Sent: *Sunday, February 26, 2017 3:50 PM *To: *freesurfer@nmr.mgh.harvard.edu *Reply To: *Freesurfer support list *Subject: *Re: [Freesurfer] Fw: PETsurfer mri_coreg problem
Dear Paul,
LTA means transformation matrix stored in .lta format.
This matrix can encode transformation between various coordinate spaces.
What coordinate systems transform this .lta from and to is specified by string in the .lta file. Typically this type could be vox2RAS, RAS2vox, vox2vox or RAS2RAS. Most typically the type is vox2vox.
The explanation of coordinate systems is specified for example here: http://freesurfer.net/fswiki/CoordinateSystems http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm
The output of freeview is only info, not error, indicating that your .lta is not of type vox2vox. I personally still use tkregister2 for checking of registration, since the freeview does not contain full functionality for checking transformations (see the warning). Therefore I have no experience with tkregisterfv and consider tkregister2 still as a "gold standard". However, if you use tkregisterfv for checkning transformation between volumes and the output is only "info", I would guess that everything is OK and you do not need to be bothered.
Btw, does the alignment of the images seem reasonable? How does it look in tkregister2?
Regards,
Antonin
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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
But what would you compare if you had these coordinates? What would the coordinates tell you?
On 2/27/17 11:01 AM, miracle ozzoude wrote:
Hello Doug, Thanks for replying. I meant like coordinate points on both images to compare (i.e., any metric different from visual inspection). Best, Paul.
On Mon, Feb 27, 2017 at 10:50 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I'm not sure what you mean. If the registration looks good, what do you need to extract? On 2/27/17 9:03 AM, miracle ozzoude wrote:Hello Antonin and Doug, I viewed it in tkregister2 and I think the co-registration worked. Is there a way to extract info from both PET and anatomical to confirm the co-registration? Best, Paul On Sun, Feb 26, 2017 at 4:49 PM, Antonin Skoch <ansk@ikem.cz <mailto:ansk@ikem.cz>> wrote: Dear Paul, I think that the transform window in freeview opens by default to enable manual refinement of registration if needed. If you are not sure, try also tkregister2. It should work to simply replace tkregisterfv by tkregister2, the command would be tkregister2 --mov your_moveable --targ your_target --reg your_lta or, if you registered your PET to freesurfer-processed subject and want also to display surfaces, you should use tkregister2, no tkregisterfv (according to the freeview warning). The command in this case would be tkregister2 --mov your_moveable --s your_subject_id --reg your_lta --surfs Antonin Hello Antonin, Thank you for your quick reply. Does this mean I should close the transform window when it opens? The alignment looks good to me, I was worried because the transform window opened and the info on the terminal window. I haven't used tkregister2 before. Do I replace tkregisterfv with tkregister2 like this " tkregister2 --mov template.nii.gz --reg template.reg.lta --surfs"? Thanks. Best, Paul Sent from my BlackBerry 10 smartphone. *From: *Antonin Skoch *Sent: *Sunday, February 26, 2017 3:50 PM *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Reply To: *Freesurfer support list *Subject: *Re: [Freesurfer] Fw: PETsurfer mri_coreg problem Dear Paul, LTA means transformation matrix stored in .lta format. This matrix can encode transformation between various coordinate spaces. What coordinate systems transform this .lta from and to is specified by string in the .lta file. Typically this type could be vox2RAS, RAS2vox, vox2vox or RAS2RAS. Most typically the type is vox2vox. The explanation of coordinate systems is specified for example here: http://freesurfer.net/fswiki/CoordinateSystems <http://freesurfer.net/fswiki/CoordinateSystems> http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm <http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm> The output of freeview is only info, not error, indicating that your .lta is not of type vox2vox. I personally still use tkregister2 for checking of registration, since the freeview does not contain full functionality for checking transformations (see the warning). Therefore I have no experience with tkregisterfv and consider tkregister2 still as a "gold standard". However, if you use tkregisterfv for checkning transformation between volumes and the output is only "info", I would guess that everything is OK and you do not need to be bothered. Btw, does the alignment of the images seem reasonable? How does it look in tkregister2? Regards, Antonin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
Hello Doug, Thanks for replying. It might help evaluate the accuracy of the co-registration. Usually, We use visual inspection (placing the crosshair on 1 image (either MRI or PET) and comparing the position of the crosshair in 1 image to another image). However, this is subjective and based on experience. I want to use a objective method to inspect the accuracy of the co-registration. Please, do you have any suggestions on how I can accomplish it? Best, Paul
On Mon, Feb 27, 2017 at 11:05 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
But what would you compare if you had these coordinates? What would the coordinates tell you?
On 2/27/17 11:01 AM, miracle ozzoude wrote:
Hello Doug, Thanks for replying. I meant like coordinate points on both images to compare (i.e., any metric different from visual inspection). Best, Paul.
On Mon, Feb 27, 2017 at 10:50 AM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
I'm not sure what you mean. If the registration looks good, what do you need to extract?
On 2/27/17 9:03 AM, miracle ozzoude wrote:
Hello Antonin and Doug,
I viewed it in tkregister2 and I think the co-registration worked. Is there a way to extract info from both PET and anatomical to confirm the co-registration? Best, Paul
On Sun, Feb 26, 2017 at 4:49 PM, Antonin Skoch ansk@ikem.cz wrote:
Dear Paul,
I think that the transform window in freeview opens by default to enable manual refinement of registration if needed.
If you are not sure, try also tkregister2. It should work to simply replace tkregisterfv by tkregister2, the command would be
tkregister2 --mov your_moveable --targ your_target --reg your_lta
or, if you registered your PET to freesurfer-processed subject and want also to display surfaces, you should use tkregister2, no tkregisterfv (according to the freeview warning). The command in this case would be
tkregister2 --mov your_moveable --s your_subject_id --reg your_lta --surfs
Antonin
Hello Antonin, Thank you for your quick reply. Does this mean I should close the transform window when it opens? The alignment looks good to me, I was worried because the transform window opened and the info on the terminal window. I haven't used tkregister2 before. Do I replace tkregisterfv with tkregister2 like this " tkregister2 --mov template.nii.gz --reg template.reg.lta --surfs"? Thanks. Best, Paul Sent from my BlackBerry 10 smartphone. *From: *Antonin Skoch *Sent: *Sunday, February 26, 2017 3:50 PM *To: *freesurfer@nmr.mgh.harvard.edu *Reply To: *Freesurfer support list *Subject: *Re: [Freesurfer] Fw: PETsurfer mri_coreg problem
Dear Paul,
LTA means transformation matrix stored in .lta format.
This matrix can encode transformation between various coordinate spaces.
What coordinate systems transform this .lta from and to is specified by string in the .lta file. Typically this type could be vox2RAS, RAS2vox, vox2vox or RAS2RAS. Most typically the type is vox2vox.
The explanation of coordinate systems is specified for example here: http://freesurfer.net/fswiki/CoordinateSystems http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm
The output of freeview is only info, not error, indicating that your .lta is not of type vox2vox. I personally still use tkregister2 for checking of registration, since the freeview does not contain full functionality for checking transformations (see the warning). Therefore I have no experience with tkregisterfv and consider tkregister2 still as a "gold standard". However, if you use tkregisterfv for checkning transformation between volumes and the output is only "info", I would guess that everything is OK and you do not need to be bothered.
Btw, does the alignment of the images seem reasonable? How does it look in tkregister2?
Regards,
Antonin
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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e du/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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
I don't think there is a better way than visual inspection. You could look at the final cost value, but that is relative, ie, you could get a bunch of subjects who you know have a good registration and create a table of the final costs, then when you get a new subject, compute the z-score of the cost based on known good values.
On 02/27/2017 11:33 AM, miracle ozzoude wrote:
Hello Doug, Thanks for replying. It might help evaluate the accuracy of the co-registration. Usually, We use visual inspection (placing the crosshair on 1 image (either MRI or PET) and comparing the position of the crosshair in 1 image to another image). However, this is subjective and based on experience. I want to use a objective method to inspect the accuracy of the co-registration. Please, do you have any suggestions on how I can accomplish it? Best, Paul
On Mon, Feb 27, 2017 at 11:05 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
But what would you compare if you had these coordinates? What would the coordinates tell you? On 2/27/17 11:01 AM, miracle ozzoude wrote:Hello Doug, Thanks for replying. I meant like coordinate points on both images to compare (i.e., any metric different from visual inspection). Best, Paul. On Mon, Feb 27, 2017 at 10:50 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: I'm not sure what you mean. If the registration looks good, what do you need to extract? On 2/27/17 9:03 AM, miracle ozzoude wrote:Hello Antonin and Doug, I viewed it in tkregister2 and I think the co-registration worked. Is there a way to extract info from both PET and anatomical to confirm the co-registration? Best, Paul On Sun, Feb 26, 2017 at 4:49 PM, Antonin Skoch <ansk@ikem.cz <mailto:ansk@ikem.cz>> wrote: Dear Paul, I think that the transform window in freeview opens by default to enable manual refinement of registration if needed. If you are not sure, try also tkregister2. It should work to simply replace tkregisterfv by tkregister2, the command would be tkregister2 --mov your_moveable --targ your_target --reg your_lta or, if you registered your PET to freesurfer-processed subject and want also to display surfaces, you should use tkregister2, no tkregisterfv (according to the freeview warning). The command in this case would be tkregister2 --mov your_moveable --s your_subject_id --reg your_lta --surfs Antonin Hello Antonin, Thank you for your quick reply. Does this mean I should close the transform window when it opens? The alignment looks good to me, I was worried because the transform window opened and the info on the terminal window. I haven't used tkregister2 before. Do I replace tkregisterfv with tkregister2 like this " tkregister2 --mov template.nii.gz --reg template.reg.lta --surfs"? Thanks. Best, Paul Sent from my BlackBerry 10 smartphone. *From: *Antonin Skoch *Sent: *Sunday, February 26, 2017 3:50 PM *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Reply To: *Freesurfer support list *Subject: *Re: [Freesurfer] Fw: PETsurfer mri_coreg problem Dear Paul, LTA means transformation matrix stored in .lta format. This matrix can encode transformation between various coordinate spaces. What coordinate systems transform this .lta from and to is specified by string in the .lta file. Typically this type could be vox2RAS, RAS2vox, vox2vox or RAS2RAS. Most typically the type is vox2vox. The explanation of coordinate systems is specified for example here: http://freesurfer.net/fswiki/CoordinateSystems <http://freesurfer.net/fswiki/CoordinateSystems> http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm <http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm> The output of freeview is only info, not error, indicating that your .lta is not of type vox2vox. I personally still use tkregister2 for checking of registration, since the freeview does not contain full functionality for checking transformations (see the warning). Therefore I have no experience with tkregisterfv and consider tkregister2 still as a "gold standard". However, if you use tkregisterfv for checkning transformation between volumes and the output is only "info", I would guess that everything is OK and you do not need to be bothered. Btw, does the alignment of the images seem reasonable? How does it look in tkregister2? Regards, Antonin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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.
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