Hi!
I am having some trouble with the motion correction step when having two volumes (NIFTI files). The average volume has not been determined correctly due to a wrong orientation/registration of the two original volumes (see http://freesurfer.nikolasborrel.com/bad_registration.tif). Is the problem caused by wrong information in the qform matrix in the header of the NIFTI file or by a bad registration in the mri_robust_template or mri_convert functions in the motion correction step?
Kind regards Nikolas Borrel-Jensen
I'm not sure about the mri_robust_template issue, but you can check the orientation by loading it in tkmedit. If the axial is axial with (nose up) and the sag is sag (with nose to the right), then the qform is right (assuming that LR is ok, which you can't check based on the direction of the nose:). doug
Nikolas Borrel-Jensen wrote:
Hi!
I am having some trouble with the motion correction step when having two volumes (NIFTI files). The average volume has not been determined correctly due to a wrong orientation/registration of the two original volumes (see http://freesurfer.nikolasborrel.com/bad_registration.tif). Is the problem caused by wrong information in the qform matrix in the header of the NIFTI file or by a bad registration in the mri_robust_template or mri_convert functions in the motion correction step?
Kind regards Nikolas Borrel-Jensen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi again.
The orientation looks correct for both volumes (001.mgz and 002.mgz). Does anyone know what is then going wrong with the registration in Freesurfer? The average volume (orig.mgz) can be seen here: http://freesurfer.nikolasborrel.com/bad_registration.tif
Kind regards Nikolas Borrel-Jensen
Hello!
I have found a solution for the problem causing the bad registration.
In Freesurfer 5.0, the function mri_robust_template is used for registration creating the output volume rawavg.mgz when using the autorecon1 flag. It turns out, that in Freesurfer 4.0, this step is performed by the function mri_motion_correct.fsl and using this function instead of mri_robust_template, the registration works perfectly! The volumes I use have different intensity levels, and it may be the reason why mri_robust_template fails, since it require that the input images should all have the same intensity level. For other volumes not failing the registration, I have noticed that the resulting volume sometimes are more blurred when using v. 5.0 than v. 4.0.
So, why is the registration step more robust in v. 4.0 than v. 5.0? Is it possible to change the autorecon1 script in v. 5.0, such that mri_motion_correct.fsl is used instead of mri_robust_template?
Kind regards Nikolas
You can run the old command and then start the processing from that step on I think.
On Mar 30, 2011, at 4:23 AM, Nikolas Borrel-Jensen nikolasborrel@gmail.com wrote:
Hello!
I have found a solution for the problem causing the bad registration.
In Freesurfer 5.0, the function mri_robust_template is used for registration creating the output volume rawavg.mgz when using the autorecon1 flag. It turns out, that in Freesurfer 4.0, this step is performed by the function mri_motion_correct.fsl and using this function instead of mri_robust_template, the registration works perfectly! The volumes I use have different intensity levels, and it may be the reason why mri_robust_template fails, since it require that the input images should all have the same intensity level. For other volumes not failing the registration, I have noticed that the resulting volume sometimes are more blurred when using v. 5.0 than v. 4.0.
So, why is the registration step more robust in v. 4.0 than v. 5.0? Is it possible to change the autorecon1 script in v. 5.0, such that mri_motion_correct.fsl is used instead of mri_robust_template?
Kind regards Nikolas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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