Hello, Freesurfer group, I am registering the fMRI results to surface using reg-feat2anat (v 1.26.2.1 2007/08/15) and tkregister2. The automatic registration catastrophically failed in the subject space, but worked fine in the standard space. The orientations of example_func.nii.gz in the subject space are flipped in any view. I use the tkmedit to view the example_func, and found the orientation is wrong. It seems Freesurfer can not read nifti header correctly. I attach the reg-feat2anat log file and an example_func.nii.gz. I found the following message from Freesurfer email list. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html Does Freesurfer have a solution for this type of problems by now?
Thank you in advance,
Xin
Hi Xin, the problem is that neither the sform nor the qform are valid. Did the message below not appear when you ran tkmedit?
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented
Fix that, and everything will work fine.
doug
Wang, Xin wrote:
Hello, Freesurfer group, I am registering the fMRI results to surface using reg-feat2anat (v 1.26.2.1 2007/08/15) and tkregister2. The automatic registration catastrophically failed in the subject space, but worked fine in the standard space. The orientations of example_func.nii.gz in the subject space are flipped in any view. I use the tkmedit to view the example_func, and found the orientation is wrong. It seems Freesurfer can not read nifti header correctly. I attach the reg-feat2anat log file and an example_func.nii.gz. I found the following message from Freesurfer email list. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html Does Freesurfer have a solution for this type of problems by now?
Thank you in advance,
Xin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you very much for your quick reply, Dr. Greve. I asked our institutional MRI center for correct information on qform and sform since the header of nifti files are created by their scripts. But I do not know what they can do to fix this problem. I will appreciate if you have any further suggestion on how to do the registration without the information on qform and sform in case I can not get them. Does convert to ANALYZE format or manually correct in tkregister2 work?
Thank you again,
Xin
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 12/15/2008 1:09 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] reg-feat2anat failed
Hi Xin, the problem is that neither the sform nor the qform are valid. Did the message below not appear when you ran tkmedit?
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented
Fix that, and everything will work fine.
doug
Wang, Xin wrote:
Hello, Freesurfer group, I am registering the fMRI results to surface using reg-feat2anat (v 1.26.2.1 2007/08/15) and tkregister2. The automatic registration catastrophically failed in the subject space, but worked fine in the standard space. The orientations of example_func.nii.gz in the subject space are flipped in any view. I use the tkmedit to view the example_func, and found the orientation is wrong. It seems Freesurfer can not read nifti header correctly. I attach the reg-feat2anat log file and an example_func.nii.gz. I found the following message from Freesurfer email list. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html Does Freesurfer have a solution for this type of problems by now?
Thank you in advance,
Xin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
There is a flag in the nifti header saying whether the qform or sform are valid, and it looks like your scripts do not set this flag. You can use mri_convert (the freesurfer program). This will create valid files that can be read into any program.
doug
Wang, Xin wrote:
Thank you very much for your quick reply, Dr. Greve. I asked our institutional MRI center for correct information on qform and sform since the header of nifti files are created by their scripts. But I do not know what they can do to fix this problem. I will appreciate if you have any further suggestion on how to do the registration without the information on qform and sform in case I can not get them. Does convert to ANALYZE format or manually correct in tkregister2 work?
Thank you again,
Xin
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 12/15/2008 1:09 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] reg-feat2anat failed
Hi Xin, the problem is that neither the sform nor the qform are valid. Did the message below not appear when you ran tkmedit?
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented
Fix that, and everything will work fine.
doug
Wang, Xin wrote:
Hello, Freesurfer group, I am registering the fMRI results to surface using reg-feat2anat (v 1.26.2.1 2007/08/15) and tkregister2. The automatic registration catastrophically failed in the subject space, but worked fine in the standard space. The orientations of example_func.nii.gz in the subject space are flipped in any view. I use the tkmedit to view the example_func, and found the orientation is wrong. It seems Freesurfer can not read nifti header correctly. I attach the reg-feat2anat log file and an example_func.nii.gz. I found the following message from Freesurfer email list. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html Does Freesurfer have a solution for this type of problems by now?
Thank you in advance,
Xin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
hello, Freesurfer group,
I try to use registration.mat files of FSL/FEAT routines, instead of anat2example_func.bat, to register the orig.mgz and example_func.nii.gz with the thinking that using initial_highres in FEAT may improve the reg. However, tkregister2 catastrophically failed to register two brains when I use --fsl flag. Modifying header of example_func with mri_convert does not solve the problem. I will appreciate any suggestion on using .mat file for registration.
second question: what is the best registration of example_func and orig.mgz? In another word, what should I check besides things in the FS tutorial when I check/modify the registration in tkregister2? Is there golden reference points I can use?
Thank you in advance for any suggestion.
Xin wang
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 12/15/2008 1:26 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] reg-feat2anat failed
There is a flag in the nifti header saying whether the qform or sform are valid, and it looks like your scripts do not set this flag. You can use mri_convert (the freesurfer program). This will create valid files that can be read into any program.
doug
Wang, Xin wrote:
Thank you very much for your quick reply, Dr. Greve. I asked our institutional MRI center for correct information on qform and sform since the header of nifti files are created by their scripts. But I do not know what they can do to fix this problem. I will appreciate if you have any further suggestion on how to do the registration without the information on qform and sform in case I can not get them. Does convert to ANALYZE format or manually correct in tkregister2 work?
Thank you again,
Xin
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 12/15/2008 1:09 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] reg-feat2anat failed
Hi Xin, the problem is that neither the sform nor the qform are valid. Did the message below not appear when you ran tkmedit?
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented
Fix that, and everything will work fine.
doug
Wang, Xin wrote:
Hello, Freesurfer group, I am registering the fMRI results to surface using reg-feat2anat (v 1.26.2.1 2007/08/15) and tkregister2. The automatic registration catastrophically failed in the subject space, but worked fine in the standard space. The orientations of example_func.nii.gz in the subject space are flipped in any view. I use the tkmedit to view the example_func, and found the orientation is wrong. It seems Freesurfer can not read nifti header correctly. I attach the reg-feat2anat log file and an example_func.nii.gz. I found the following message from Freesurfer email list. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html Does Freesurfer have a solution for this type of problems by now?
Thank you in advance,
Xin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Hi Xin, I'm not sure what's going wrong here, I think I need more info. Can you follow the steps in surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?
doug
Wang, Xin wrote:
hello, Freesurfer group,
I try to use registration.mat files of FSL/FEAT routines, instead of anat2example_func.bat, to register the orig.mgz and example_func.nii.gz with the thinking that using initial_highres in FEAT may improve the reg. However, tkregister2 catastrophically failed to register two brains when I use --fsl flag. Modifying header of example_func with mri_convert does not solve the problem. I will appreciate any suggestion on using .mat file for registration.
second question: what is the best registration of example_func and orig.mgz? In another word, what should I check besides things in the FS tutorial when I check/modify the registration in tkregister2? Is there golden reference points I can use?
Thank you in advance for any suggestion.
Xin wang
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 12/15/2008 1:26 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] reg-feat2anat failed
There is a flag in the nifti header saying whether the qform or sform are valid, and it looks like your scripts do not set this flag. You can use mri_convert (the freesurfer program). This will create valid files that can be read into any program.
doug
Wang, Xin wrote:
Thank you very much for your quick reply, Dr. Greve. I asked our institutional MRI center for correct information on qform and sform since the header of nifti files are created by their scripts. But I do not know what they can do to fix this problem. I will appreciate if you have any further suggestion on how to do the registration without the information on qform and sform in case I can not get them. Does convert to ANALYZE format or manually correct in tkregister2 work?
Thank you again,
Xin
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 12/15/2008 1:09 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] reg-feat2anat failed
Hi Xin, the problem is that neither the sform nor the qform are valid. Did the message below not appear when you ran tkmedit?
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented
Fix that, and everything will work fine.
doug
Wang, Xin wrote:
Hello, Freesurfer group, I am registering the fMRI results to surface using reg-feat2anat (v 1.26.2.1 2007/08/15) and tkregister2. The automatic registration catastrophically failed in the subject space, but worked fine in the standard space. The orientations of example_func.nii.gz in the subject space are flipped in any view. I use the tkmedit to view the example_func, and found the orientation is wrong. It seems Freesurfer can not read nifti header correctly. I attach the reg-feat2anat log file and an example_func.nii.gz. I found the following message from Freesurfer email list.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html
Does Freesurfer have a solution for this type of problems by now?
Thank you in advance,
Xin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Wang, Xin