Dear list,
After fixing the Talairach transform automatically, (by mri_convert , the final objective funciton value is fine, ca.0.06) So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and it looked pretty fine with tkregister2. Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, and then viewed it with tkmedit and tkreigister2. Under tkregister2 the talairach transform looks pretty good but not the target.(the oreientations of the target are totally mixed up, those of the moveble volume are correct).
I checked orig.mgz are also mixed up, coronal becomes sagittal, sagittal becomes horizontal, etc. Any suggestions about this ?
Thanks.
Jackie
Hi,
I'm a little confused, so please correct me if I've made the wrong assumptions. It sounds like your problem is becuase your orig volume is in the wrong orientation when you view it in tkmedit (ie., the coronal view in tkmedit does not show a coronal view, but shows the sagital view). It seems, also, that this was not always the case - until you fixed the talairach transform. Can you give me the exact mri_convert command that you used to fix the talaraich?
What type of scans are these? Siemens, GE? what format were they in before they were in mgz? It may be the case that you need to re-convert them to correct the orientation. To do this, though, you'd need to be sure you could identify the right side from the left side. You can use some switched in mri_convert - I'd be glad to help you figure that command out if this ends up to be the problem.
Jenni
On Mon, 30 Apr 2007 Chuan.Chih.Yang@rwth-aachen.de wrote:
Dear list,
After fixing the Talairach transform automatically, (by mri_convert , the final objective funciton value is fine, ca.0.06) So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and it looked pretty fine with tkregister2. Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, and then viewed it with tkmedit and tkreigister2. Under tkregister2 the talairach transform looks pretty good but not the target.(the oreientations of the target are totally mixed up, those of the moveble volume are correct).
I checked orig.mgz are also mixed up, coronal becomes sagittal, sagittal becomes horizontal, etc. Any suggestions about this ?
Thanks.
Jackie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jenni,
The orig volume is in the correct orientation when I viewed it with tikmedit. But after I fixed the Talairach transform by using mri_convert T1.mgz T1.mnc , mritotal -protocol icbm T1.mnc T1.xfm.,(and I viewed it in tkregister2, which looks quite fine), then I ran recon-all -subjid xxxx -autorecon1 -notalairach . But after this step, the orientation of the target volume is mixed up, same as the orig.mgz volume.(before fixing Talairach the orig voulme are correct) p.s the orientation of the moveble volumes are correct after fixing
They are nifti files and acquired by Siemens Sonata. (We already used the avwswapdim to reorient them before running, and we also put mark on the brain so that we could tell L and R)
Thank you for your help! Jackie
Jenni Pacheco schrieb:
Hi,
I'm a little confused, so please correct me if I've made the wrong assumptions. It sounds like your problem is becuase your orig volume is in the wrong orientation when you view it in tkmedit (ie., the coronal view in tkmedit does not show a coronal view, but shows the sagital view). It seems, also, that this was not always the case - until you fixed the talairach transform. Can you give me the exact mri_convert command that you used to fix the talaraich?
What type of scans are these? Siemens, GE? what format were they in before they were in mgz? It may be the case that you need to re-convert them to correct the orientation. To do this, though, you'd need to be sure you could identify the right side from the left side. You can use some switched in mri_convert - I'd be glad to help you figure that command out if this ends up to be the problem.
Jenni
On Mon, 30 Apr 2007 Chuan.Chih.Yang@rwth-aachen.de wrote:
Dear list,
After fixing the Talairach transform automatically, (by mri_convert , the final objective funciton value is fine, ca.0.06) So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and it looked pretty fine with tkregister2. Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, and then viewed it with tkmedit and tkreigister2. Under tkregister2 the talairach transform looks pretty good but not the target.(the oreientations of the target are totally mixed up, those of the moveble volume are correct).
I checked orig.mgz are also mixed up, coronal becomes sagittal, sagittal becomes horizontal, etc. Any suggestions about this ?
Thanks.
Jackie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jackie,
you need to rename the T1.xfm to be talairach.xfm and put it in the mri/transforms dir.
When you say "after this step, the orientation of the target volume is mixed up" do you mean after applying the tal transform? The orientation of all the .mgz (e.g. orig.mgz, T1.mgz, brain.mgz) should be identical.
cheers, Bruce
On Mon, 30 Apr 2007, Jackie_rwth wrote:
Hi Jenni,
The orig volume is in the correct orientation when I viewed it with tikmedit. But after I fixed the Talairach transform by using mri_convert T1.mgz T1.mnc , mritotal -protocol icbm T1.mnc T1.xfm.,(and I viewed it in tkregister2, which looks quite fine), then I ran recon-all -subjid xxxx -autorecon1 -notalairach . But after this step, the orientation of the target volume is mixed up, same as the orig.mgz volume.(before fixing Talairach the orig voulme are correct) p.s the orientation of the moveble volumes are correct after fixing
They are nifti files and acquired by Siemens Sonata. (We already used the avwswapdim to reorient them before running, and we also put mark on the brain so that we could tell L and R)
Thank you for your help! Jackie
Jenni Pacheco schrieb:
Hi,
I'm a little confused, so please correct me if I've made the wrong assumptions. It sounds like your problem is becuase your orig volume is in the wrong orientation when you view it in tkmedit (ie., the coronal view in tkmedit does not show a coronal view, but shows the sagital view). It seems, also, that this was not always the case - until you fixed the talairach transform. Can you give me the exact mri_convert command that you used to fix the talaraich?
What type of scans are these? Siemens, GE? what format were they in before they were in mgz? It may be the case that you need to re-convert them to correct the orientation. To do this, though, you'd need to be sure you could identify the right side from the left side. You can use some switched in mri_convert - I'd be glad to help you figure that command out if this ends up to be the problem.
Jenni
On Mon, 30 Apr 2007 Chuan.Chih.Yang@rwth-aachen.de wrote:
Dear list,
After fixing the Talairach transform automatically, (by mri_convert , the final objective funciton value is fine, ca.0.06) So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and it looked pretty fine with tkregister2. Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, and then viewed it with tkmedit and tkreigister2. Under tkregister2 the talairach transform looks pretty good but not the target.(the oreientations of the target are totally mixed up, those of the moveble volume are correct).
I checked orig.mgz are also mixed up, coronal becomes sagittal, sagittal becomes horizontal, etc. Any suggestions about this ?
Thanks.
Jackie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Hi Bruce,
Yes, I have renamed the T1.xfm to talairach.xfm and put it in mri/transforms dir, and also when I ran autorecon1 and put the - notalairach flag after fixing.
Yes, I mean after fixing the tal transform.
The orientation of the orig.mgz , T1.mgz, and brain.mgz are in another orietation as the "movebel volume"(the one after tal transform). eg. when I used tkregister2 the COMPARE button to check the tal transfrom, the orietations of two images ( one is after tal transform, the other is T1.mgz) are not identical, (when I pressed "coronal" button, the movble voulme is in coronal direction but the target volume is in horozontal direction, ...etc.)
And then I used tkmedit to check the orig-, T1-, and brain.mgz, they are all in the same situation but the wrong one.(coronal view became horozontal view, horozontal view become sagittal view , etc...)
Any sugguestion will be helpful! cheers, Jackie
Bruce Fischl schrieb:
Hi Jackie,
you need to rename the T1.xfm to be talairach.xfm and put it in the mri/transforms dir.
When you say "after this step, the orientation of the target volume is mixed up" do you mean after applying the tal transform? The orientation of all the .mgz (e.g. orig.mgz, T1.mgz, brain.mgz) should be identical.
cheers, Bruce
On Mon, 30 Apr 2007, Jackie_rwth wrote:
Hi Jenni,
The orig volume is in the correct orientation when I viewed it with tikmedit. But after I fixed the Talairach transform by using mri_convert T1.mgz T1.mnc , mritotal -protocol icbm T1.mnc T1.xfm.,(and I viewed it in tkregister2, which looks quite fine), then I ran recon-all -subjid xxxx -autorecon1 -notalairach . But after this step, the orientation of the target volume is mixed up, same as the orig.mgz volume.(before fixing Talairach the orig voulme are correct) p.s the orientation of the moveble volumes are correct after fixing
They are nifti files and acquired by Siemens Sonata. (We already used the avwswapdim to reorient them before running, and we also put mark on the brain so that we could tell L and R)
Thank you for your help! Jackie
Jenni Pacheco schrieb:
Hi,
I'm a little confused, so please correct me if I've made the wrong assumptions. It sounds like your problem is becuase your orig volume is in the wrong orientation when you view it in tkmedit (ie., the coronal view in tkmedit does not show a coronal view, but shows the sagital view). It seems, also, that this was not always the case
- until you fixed the talairach transform. Can you give me the
exact mri_convert command that you used to fix the talaraich?
What type of scans are these? Siemens, GE? what format were they in before they were in mgz? It may be the case that you need to re-convert them to correct the orientation. To do this, though, you'd need to be sure you could identify the right side from the left side. You can use some switched in mri_convert - I'd be glad to help you figure that command out if this ends up to be the problem.
Jenni
On Mon, 30 Apr 2007 Chuan.Chih.Yang@rwth-aachen.de wrote:
Dear list,
After fixing the Talairach transform automatically, (by mri_convert , the final objective funciton value is fine, ca.0.06) So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and it looked pretty fine with tkregister2. Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, and then viewed it with tkmedit and tkreigister2. Under tkregister2 the talairach transform looks pretty good but not the target.(the oreientations of the target are totally mixed up, those of the moveble volume are correct).
I checked orig.mgz are also mixed up, coronal becomes sagittal, sagittal becomes horizontal, etc. Any suggestions about this ?
Thanks.
Jackie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Hi Jackie,
What command line are you using to open tkregister2 to check your talairach transform? I'm not sure that the moveable volume is really the one after talairach transform - likely (depending on the command you used) the moveable volume is the talairach subject, the target volume that you want your subject to match.
Can you send your command line.
Thanks, Jenni -----Original Message----- From: Jackie_rwth [mailto:chuan.chih.yang@rwth-aachen.de] Sent: Tuesday, May 01, 2007 3:02 AM To: Bruce Fischl Cc: Jenni Pacheco; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach transform
Hi Bruce,
Yes, I have renamed the T1.xfm to talairach.xfm and put it in mri/transforms dir, and also when I ran autorecon1 and put the - notalairach flag after fixing.
Yes, I mean after fixing the tal transform.
The orientation of the orig.mgz , T1.mgz, and brain.mgz are in another orietation as the "movebel volume"(the one after tal transform). eg. when I used tkregister2 the COMPARE button to check the tal transfrom, the orietations of two images ( one is after tal transform, the other is T1.mgz) are not identical, (when I pressed "coronal" button, the movble voulme is in coronal direction but the target volume is in horozontal direction, ...etc.)
And then I used tkmedit to check the orig-, T1-, and brain.mgz, they are all in the same situation but the wrong one.(coronal view became horozontal view, horozontal view become sagittal view , etc...)
Any sugguestion will be helpful! cheers, Jackie
Bruce Fischl schrieb:
Hi Jackie,
you need to rename the T1.xfm to be talairach.xfm and put it in the mri/transforms dir.
When you say "after this step, the orientation of the target volume is mixed up" do you mean after applying the tal transform? The orientation of all the .mgz (e.g. orig.mgz, T1.mgz, brain.mgz) should be identical.
cheers, Bruce
On Mon, 30 Apr 2007, Jackie_rwth wrote:
Hi Jenni,
The orig volume is in the correct orientation when I viewed it with tikmedit. But after I fixed the Talairach transform by using mri_convert T1.mgz T1.mnc , mritotal -protocol icbm T1.mnc T1.xfm.,(and I viewed it in tkregister2, which looks quite fine), then I ran recon-all -subjid xxxx -autorecon1 -notalairach . But after this step, the orientation of the target volume is mixed up, same as the orig.mgz volume.(before fixing Talairach the orig voulme are correct) p.s the orientation of the moveble volumes are correct after fixing
They are nifti files and acquired by Siemens Sonata. (We already used the avwswapdim to reorient them before running, and we also put mark on the brain so that we could tell L and R)
Thank you for your help! Jackie
Jenni Pacheco schrieb:
Hi,
I'm a little confused, so please correct me if I've made the wrong assumptions. It sounds like your problem is becuase your orig volume is in the wrong orientation when you view it in tkmedit (ie., the coronal view in tkmedit does not show a coronal view, but shows the sagital view). It seems, also, that this was not always the case
- until you fixed the talairach transform. Can you give me the
exact mri_convert command that you used to fix the talaraich?
What type of scans are these? Siemens, GE? what format were they in before they were in mgz? It may be the case that you need to re-convert them to correct the orientation. To do this, though, you'd need to be sure you could identify the right side from the left side. You can use some switched in mri_convert - I'd be glad to help you figure that command out if this ends up to be the problem.
Jenni
On Mon, 30 Apr 2007 Chuan.Chih.Yang@rwth-aachen.de wrote:
Dear list,
After fixing the Talairach transform automatically, (by mri_convert , the final objective funciton value is fine, ca.0.06) So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and it looked pretty fine with tkregister2. Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, and then viewed it with tkmedit and tkreigister2. Under tkregister2 the talairach transform looks pretty good but not the target.(the oreientations of the target are totally mixed up, those of the moveble volume are correct).
I checked orig.mgz are also mixed up, coronal becomes sagittal, sagittal becomes horizontal, etc. Any suggestions about this ?
Thanks.
Jackie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Hi Jenni,
This is the command line I used for checking talairach transform. tkregister2 --mgz --s xxxxx --fstal.
cheers, Jackie
Jenni Pacheco schrieb:
Hi Jackie,
What command line are you using to open tkregister2 to check your talairach transform? I'm not sure that the moveable volume is really the one after talairach transform - likely (depending on the command you used) the moveable volume is the talairach subject, the target volume that you want your subject to match.
Can you send your command line.
Thanks, Jenni -----Original Message----- From: Jackie_rwth [mailto:chuan.chih.yang@rwth-aachen.de] Sent: Tuesday, May 01, 2007 3:02 AM To: Bruce Fischl Cc: Jenni Pacheco; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach transform
Hi Bruce,
Yes, I have renamed the T1.xfm to talairach.xfm and put it in mri/transforms dir, and also when I ran autorecon1 and put the - notalairach flag after fixing.
Yes, I mean after fixing the tal transform.
The orientation of the orig.mgz , T1.mgz, and brain.mgz are in another orietation as the "movebel volume"(the one after tal transform). eg. when I used tkregister2 the COMPARE button to check the tal transfrom, the orietations of two images ( one is after tal transform, the other is T1.mgz) are not identical, (when I pressed "coronal" button, the movble voulme is in coronal direction but the target volume is in horozontal direction, ...etc.)
And then I used tkmedit to check the orig-, T1-, and brain.mgz, they are all in the same situation but the wrong one.(coronal view became horozontal view, horozontal view become sagittal view , etc...)
Any sugguestion will be helpful! cheers, Jackie
Bruce Fischl schrieb:
Hi Jackie,
you need to rename the T1.xfm to be talairach.xfm and put it in the mri/transforms dir.
When you say "after this step, the orientation of the target volume is mixed up" do you mean after applying the tal transform? The orientation of all the .mgz (e.g. orig.mgz, T1.mgz, brain.mgz) should be identical.
cheers, Bruce
On Mon, 30 Apr 2007, Jackie_rwth wrote:
Hi Jenni,
The orig volume is in the correct orientation when I viewed it with tikmedit. But after I fixed the Talairach transform by using mri_convert T1.mgz T1.mnc , mritotal -protocol icbm T1.mnc T1.xfm.,(and I viewed it in tkregister2, which looks quite fine), then I ran recon-all -subjid xxxx -autorecon1 -notalairach . But after this step, the orientation of the target volume is mixed up, same as the orig.mgz volume.(before fixing Talairach the orig voulme are correct) p.s the orientation of the moveble volumes are correct after fixing
They are nifti files and acquired by Siemens Sonata. (We already used the avwswapdim to reorient them before running, and we also put mark on the brain so that we could tell L and R)
Thank you for your help! Jackie
Jenni Pacheco schrieb:
Hi,
I'm a little confused, so please correct me if I've made the wrong assumptions. It sounds like your problem is becuase your orig volume is in the wrong orientation when you view it in tkmedit (ie., the coronal view in tkmedit does not show a coronal view, but shows the sagital view). It seems, also, that this was not always the case
- until you fixed the talairach transform. Can you give me the
exact mri_convert command that you used to fix the talaraich?
What type of scans are these? Siemens, GE? what format were they in before they were in mgz? It may be the case that you need to re-convert them to correct the orientation. To do this, though, you'd need to be sure you could identify the right side from the left side. You can use some switched in mri_convert - I'd be glad to help you figure that command out if this ends up to be the problem.
Jenni
On Mon, 30 Apr 2007 Chuan.Chih.Yang@rwth-aachen.de wrote:
Dear list,
After fixing the Talairach transform automatically, (by mri_convert , the final objective funciton value is fine, ca.0.06) So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and it looked pretty fine with tkregister2. Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, and then viewed it with tkmedit and tkreigister2. Under tkregister2 the talairach transform looks pretty good but not the target.(the oreientations of the target are totally mixed up, those of the moveble volume are correct).
I checked orig.mgz are also mixed up, coronal becomes sagittal, sagittal becomes horizontal, etc. Any suggestions about this ?
Thanks.
Jackie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Hi Jackie,
So that command will bring up your subject and the talairach subject and allow you to try and register them - it is not something before and after talairach.
Going back to the problem of things oriented the wrong way. All the volumes (orig.mgz, brainmask.mgz, T1.mgz etc) should be oriented the same as each other - is this true?
Are you seeing them oriented correctly in tkmedit but incorrectly in tkregister2?
Jenni
On Tue, 1 May 2007, Jackie_rwth wrote:
Hi Jenni,
This is the command line I used for checking talairach transform. tkregister2 --mgz --s xxxxx --fstal.
cheers, Jackie
Jenni Pacheco schrieb:
Hi Jackie,
What command line are you using to open tkregister2 to check your talairach transform? I'm not sure that the moveable volume is really the one after talairach transform - likely (depending on the command you used) the moveable volume is the talairach subject, the target volume that you want your subject to match.
Can you send your command line.
Thanks, Jenni -----Original Message----- From: Jackie_rwth [mailto:chuan.chih.yang@rwth-aachen.de] Sent: Tuesday, May 01, 2007 3:02 AM To: Bruce Fischl Cc: Jenni Pacheco; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach transform
Hi Bruce,
Yes, I have renamed the T1.xfm to talairach.xfm and put it in mri/transforms dir, and also when I ran autorecon1 and put the - notalairach flag after fixing.
Yes, I mean after fixing the tal transform.
The orientation of the orig.mgz , T1.mgz, and brain.mgz are in another orietation as the "movebel volume"(the one after tal transform). eg. when I used tkregister2 the COMPARE button to check the tal transfrom, the orietations of two images ( one is after tal transform, the other is T1.mgz) are not identical, (when I pressed "coronal" button, the movble voulme is in coronal direction but the target volume is in horozontal direction, ...etc.)
And then I used tkmedit to check the orig-, T1-, and brain.mgz, they are all in the same situation but the wrong one.(coronal view became horozontal view, horozontal view become sagittal view , etc...)
Any sugguestion will be helpful! cheers, Jackie
Bruce Fischl schrieb:
Hi Jackie,
you need to rename the T1.xfm to be talairach.xfm and put it in the mri/transforms dir.
When you say "after this step, the orientation of the target volume is mixed up" do you mean after applying the tal transform? The orientation of all the .mgz (e.g. orig.mgz, T1.mgz, brain.mgz) should be identical.
cheers, Bruce
On Mon, 30 Apr 2007, Jackie_rwth wrote:
Hi Jenni,
The orig volume is in the correct orientation when I viewed it with tikmedit. But after I fixed the Talairach transform by using mri_convert T1.mgz T1.mnc , mritotal -protocol icbm T1.mnc T1.xfm.,(and I viewed it in tkregister2, which looks quite fine), then I ran recon-all -subjid xxxx -autorecon1 -notalairach . But after this step, the orientation of the target volume is mixed up, same as the orig.mgz volume.(before fixing Talairach the orig voulme are correct) p.s the orientation of the moveble volumes are correct after fixing
They are nifti files and acquired by Siemens Sonata. (We already used the avwswapdim to reorient them before running, and we also put mark on the brain so that we could tell L and R)
Thank you for your help! Jackie
Jenni Pacheco schrieb:
Hi,
I'm a little confused, so please correct me if I've made the wrong assumptions. It sounds like your problem is becuase your orig volume is in the wrong orientation when you view it in tkmedit (ie., the coronal view in tkmedit does not show a coronal view, but shows the sagital view). It seems, also, that this was not always the case - until you fixed the talairach transform. Can you give me the exact mri_convert command that you used to fix the talaraich?
What type of scans are these? Siemens, GE? what format were they in before they were in mgz? It may be the case that you need to re-convert them to correct the orientation. To do this, though, you'd need to be sure you could identify the right side from the left side. You can use some switched in mri_convert - I'd be glad to help you figure that command out if this ends up to be the problem.
Jenni
On Mon, 30 Apr 2007 Chuan.Chih.Yang@rwth-aachen.de wrote:
Dear list,
After fixing the Talairach transform automatically, (by mri_convert , the final objective funciton value is fine, ca.0.06) So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and it looked pretty fine with tkregister2. Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, and then viewed it with tkmedit and tkreigister2. Under tkregister2 the talairach transform looks pretty good but not the target.(the oreientations of the target are totally mixed up, those of the moveble volume are correct).
I checked orig.mgz are also mixed up, coronal becomes sagittal, sagittal becomes horizontal, etc. Any suggestions about this ?
Thanks.
Jackie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Hi Jenni, all the mgz. are all in the wrong orientaions both in tkregister2 and tkmedit. except the talairach volume which I fixed, they are in the correct orientation. Jackie
Jenni Pacheco schrieb:
Hi Jackie,
So that command will bring up your subject and the talairach subject and allow you to try and register them - it is not something before and after talairach.
Going back to the problem of things oriented the wrong way. All the volumes (orig.mgz, brainmask.mgz, T1.mgz etc) should be oriented the same as each other - is this true?
Are you seeing them oriented correctly in tkmedit but incorrectly in tkregister2?
Jenni
On Tue, 1 May 2007, Jackie_rwth wrote:
Hi Jenni,
This is the command line I used for checking talairach transform. tkregister2 --mgz --s xxxxx --fstal.
cheers, Jackie
Jenni Pacheco schrieb:
Hi Jackie,
What command line are you using to open tkregister2 to check your talairach transform? I'm not sure that the moveable volume is really the one after talairach transform - likely (depending on the command you used) the moveable volume is the talairach subject, the target volume that you want your subject to match.
Can you send your command line.
Thanks, Jenni -----Original Message----- From: Jackie_rwth [mailto:chuan.chih.yang@rwth-aachen.de] Sent: Tuesday, May 01, 2007 3:02 AM To: Bruce Fischl Cc: Jenni Pacheco; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach transform
Hi Bruce,
Yes, I have renamed the T1.xfm to talairach.xfm and put it in mri/transforms dir, and also when I ran autorecon1 and put the - notalairach flag after fixing.
Yes, I mean after fixing the tal transform.
The orientation of the orig.mgz , T1.mgz, and brain.mgz are in another orietation as the "movebel volume"(the one after tal transform). eg. when I used tkregister2 the COMPARE button to check the tal transfrom, the orietations of two images ( one is after tal transform, the other is T1.mgz) are not identical, (when I pressed "coronal" button, the movble voulme is in coronal direction but the target volume is in horozontal direction, ...etc.)
And then I used tkmedit to check the orig-, T1-, and brain.mgz, they are all in the same situation but the wrong one.(coronal view became horozontal view, horozontal view become sagittal view , etc...)
Any sugguestion will be helpful! cheers, Jackie
Bruce Fischl schrieb:
Hi Jackie,
you need to rename the T1.xfm to be talairach.xfm and put it in the mri/transforms dir.
When you say "after this step, the orientation of the target volume is mixed up" do you mean after applying the tal transform? The orientation of all the .mgz (e.g. orig.mgz, T1.mgz, brain.mgz) should be identical.
cheers, Bruce
On Mon, 30 Apr 2007, Jackie_rwth wrote:
Hi Jenni,
The orig volume is in the correct orientation when I viewed it with tikmedit. But after I fixed the Talairach transform by using mri_convert T1.mgz T1.mnc , mritotal -protocol icbm T1.mnc T1.xfm.,(and I viewed it in tkregister2, which looks quite fine), then I ran recon-all -subjid xxxx -autorecon1 -notalairach . But after this step, the orientation of the target volume is mixed up, same as the orig.mgz volume.(before fixing Talairach the orig voulme are correct) p.s the orientation of the moveble volumes are correct after fixing
They are nifti files and acquired by Siemens Sonata. (We already used the avwswapdim to reorient them before running, and we also put mark on the brain so that we could tell L and R)
Thank you for your help! Jackie
Jenni Pacheco schrieb:
Hi,
I'm a little confused, so please correct me if I've made the wrong assumptions. It sounds like your problem is becuase your orig volume is in the wrong orientation when you view it in tkmedit (ie., the coronal view in tkmedit does not show a coronal view, but shows the sagital view). It seems, also, that this was not always the case - until you fixed the talairach transform. Can you give me the exact mri_convert command that you used to fix the talaraich?
What type of scans are these? Siemens, GE? what format were they in before they were in mgz? It may be the case that you need to re-convert them to correct the orientation. To do this, though, you'd need to be sure you could identify the right side from the left side. You can use some switched in mri_convert - I'd be glad to help you figure that command out if this ends up to be the problem.
Jenni
On Mon, 30 Apr 2007 Chuan.Chih.Yang@rwth-aachen.de wrote:
> Dear list, > > After fixing the Talairach transform automatically, (by > mri_convert , the final objective funciton value is fine, ca.0.06) > So I replaced the talairach.xfm with T1.xfm and named it as > talairach.xfm, and it looked pretty fine with tkregister2. > Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, > and then viewed it with tkmedit and tkreigister2. > Under tkregister2 the talairach transform looks pretty good but > not the target.(the oreientations of the target are totally > mixed up, > those of the moveble volume are correct). > > I checked orig.mgz are also mixed up, coronal becomes sagittal, > sagittal becomes horizontal, etc. > Any suggestions about this ? > > Thanks. > > Jackie > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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
okay, let's go back to the beginning then. How did you generate the orig.mgz volume? What format was the input data in? If the orig.mgz has the wrong orientation then everything will fail. In general we are pretty good about reading the orientation info out of the image header, so something is pretty wrong.
On Tue, 1 May 2007, Jackie_rwth wrote:
Hi Jenni, all the mgz. are all in the wrong orientaions both in tkregister2 and tkmedit. except the talairach volume which I fixed, they are in the correct orientation. Jackie
Jenni Pacheco schrieb:
Hi Jackie,
So that command will bring up your subject and the talairach subject and allow you to try and register them - it is not something before and after talairach.
Going back to the problem of things oriented the wrong way. All the volumes (orig.mgz, brainmask.mgz, T1.mgz etc) should be oriented the same as each other - is this true?
Are you seeing them oriented correctly in tkmedit but incorrectly in tkregister2?
Jenni
On Tue, 1 May 2007, Jackie_rwth wrote:
Hi Jenni,
This is the command line I used for checking talairach transform. tkregister2 --mgz --s xxxxx --fstal.
cheers, Jackie
Jenni Pacheco schrieb:
Hi Jackie,
What command line are you using to open tkregister2 to check your talairach transform? I'm not sure that the moveable volume is really the one after talairach transform - likely (depending on the command you used) the moveable volume is the talairach subject, the target volume that you want your subject to match.
Can you send your command line.
Thanks, Jenni -----Original Message----- From: Jackie_rwth [mailto:chuan.chih.yang@rwth-aachen.de] Sent: Tuesday, May 01, 2007 3:02 AM To: Bruce Fischl Cc: Jenni Pacheco; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach transform
Hi Bruce,
Yes, I have renamed the T1.xfm to talairach.xfm and put it in mri/transforms dir, and also when I ran autorecon1 and put the - notalairach flag after fixing.
Yes, I mean after fixing the tal transform.
The orientation of the orig.mgz , T1.mgz, and brain.mgz are in another orietation as the "movebel volume"(the one after tal transform). eg. when I used tkregister2 the COMPARE button to check the tal transfrom, the orietations of two images ( one is after tal transform, the other is T1.mgz) are not identical, (when I pressed "coronal" button, the movble voulme is in coronal direction but the target volume is in horozontal direction, ...etc.)
And then I used tkmedit to check the orig-, T1-, and brain.mgz, they are all in the same situation but the wrong one.(coronal view became horozontal view, horozontal view become sagittal view , etc...)
Any sugguestion will be helpful! cheers, Jackie
Bruce Fischl schrieb:
Hi Jackie,
you need to rename the T1.xfm to be talairach.xfm and put it in the mri/transforms dir.
When you say "after this step, the orientation of the target volume is mixed up" do you mean after applying the tal transform? The orientation of all the .mgz (e.g. orig.mgz, T1.mgz, brain.mgz) should be identical.
cheers, Bruce
On Mon, 30 Apr 2007, Jackie_rwth wrote:
Hi Jenni,
The orig volume is in the correct orientation when I viewed it with tikmedit. But after I fixed the Talairach transform by using mri_convert T1.mgz T1.mnc , mritotal -protocol icbm T1.mnc T1.xfm.,(and I viewed it in tkregister2, which looks quite fine), then I ran recon-all -subjid xxxx -autorecon1 -notalairach . But after this step, the orientation of the target volume is mixed up, same as the orig.mgz volume.(before fixing Talairach the orig voulme are correct) p.s the orientation of the moveble volumes are correct after fixing
They are nifti files and acquired by Siemens Sonata. (We already used the avwswapdim to reorient them before running, and we also put mark on the brain so that we could tell L and R)
Thank you for your help! Jackie
Jenni Pacheco schrieb:
> Hi, > > I'm a little confused, so please correct me if I've made the wrong > assumptions. It sounds like your problem is becuase your orig volume > is in the wrong orientation when you view it in tkmedit (ie., the > coronal view in tkmedit does not show a coronal view, but shows the > sagital view). It seems, also, that this was not always the case - > until you fixed the talairach transform. Can you give me the exact > mri_convert command that you used to fix the talaraich? > > What type of scans are these? Siemens, GE? what format were they in > before they were in mgz? It may be the case that you need to > re-convert them to correct the orientation. To do this, though, you'd > need to be sure you could identify the right side from the left side. > You can use some switched in mri_convert - I'd be glad to help you > figure that command out if this ends up to be the problem. > > Jenni > > > On Mon, 30 Apr 2007 Chuan.Chih.Yang@rwth-aachen.de wrote: > > >> Dear list, >> >> After fixing the Talairach transform automatically, (by mri_convert , >> the final objective funciton value is fine, ca.0.06) >> So I replaced the talairach.xfm with T1.xfm and named it as >> talairach.xfm, and it looked pretty fine with tkregister2. >> Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, and >> then viewed it with tkmedit and tkreigister2. >> Under tkregister2 the talairach transform looks pretty good but not >> the target.(the oreientations of the target are totally mixed up, >> those of the moveble volume are correct). >> >> I checked orig.mgz are also mixed up, coronal becomes sagittal, >> sagittal becomes horizontal, etc. >> Any suggestions about this ? >> >> Thanks. >> >> Jackie >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Chuan.Chih.Yang＠rwth-aachen.de -
Jackie_rwth
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Jenni Pacheco