Hi Freesurfers, I want to convert a freesurfer label (amygdala aseg) to a ROI (nii file?) that I can use (overlay) in SPM. I ran mri_label2vol and then mri_convert from .mgz to .nii However, the label looks a little off, and I am wondering if I need to do some sort of transformation since Freesurfer works with the Talairach and SPM works with the MNI. In SPM, I registered the BOLD images to the T1 structural image generated in Freesurfer (after running mri_convert .mgz to .img). Does this conversion require a transformation?
Thanks for your help.
Regards, Amy
what as your label2vol command? specifically, you need to have the proper registration matrix, which is probably the problem. btw, you can use mri_label2vol to convert directly to nii.
doug
amyr@nmr.mgh.harvard.edu wrote:
Hi Freesurfers, I want to convert a freesurfer label (amygdala aseg) to a ROI (nii file?) that I can use (overlay) in SPM. I ran mri_label2vol and then mri_convert from .mgz to .nii However, the label looks a little off, and I am wondering if I need to do some sort of transformation since Freesurfer works with the Talairach and SPM works with the MNI. In SPM, I registered the BOLD images to the T1 structural image generated in Freesurfer (after running mri_convert .mgz to .img). Does this conversion require a transformation?
Thanks for your help.
Regards, Amy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I used this command:
mri_label2vol --label rh_amy_aseg.label --temp ../mri/brainmask.mgz --o rh_amy_aseg.mgz
I don't know what registration matrix to use or how to generate one.
Amy
what as your label2vol command? specifically, you need to have the proper registration matrix, which is probably the problem. btw, you can use mri_label2vol to convert directly to nii.
doug
amyr@nmr.mgh.harvard.edu wrote:
Hi Freesurfers, I want to convert a freesurfer label (amygdala aseg) to a ROI (nii file?) that I can use (overlay) in SPM. I ran mri_label2vol and then mri_convert from .mgz to .nii However, the label looks a little off, and I am wondering if I need to do some sort of transformation since Freesurfer works with the Talairach and SPM works with the MNI. In SPM, I registered the BOLD images to the T1 structural image generated in Freesurfer (after running mri_convert .mgz to .img). Does this conversion require a transformation?
Thanks for your help.
Regards, Amy
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
To use this cmd in this way, the label must have been created on the individual subject, if so, then rh_amy_aseg.mgz will be aligned with the brainmask.mgz. Which subject is this? If fsaverage, then it's mni305, which won't line up with mni152 in spm. To do this, spec $FREESURFER_HOME/average/mni152.register.dat as the registration file, and spec the mni152 brain as the template.
doug
amyr@nmr.mgh.harvard.edu wrote:
I used this command:
mri_label2vol --label rh_amy_aseg.label --temp ../mri/brainmask.mgz --o rh_amy_aseg.mgz
I don't know what registration matrix to use or how to generate one.
Amy
what as your label2vol command? specifically, you need to have the proper registration matrix, which is probably the problem. btw, you can use mri_label2vol to convert directly to nii.
doug
amyr@nmr.mgh.harvard.edu wrote:
Hi Freesurfers, I want to convert a freesurfer label (amygdala aseg) to a ROI (nii file?) that I can use (overlay) in SPM. I ran mri_label2vol and then mri_convert from .mgz to .nii However, the label looks a little off, and I am wondering if I need to do some sort of transformation since Freesurfer works with the Talairach and SPM works with the MNI. In SPM, I registered the BOLD images to the T1 structural image generated in Freesurfer (after running mri_convert .mgz to .img). Does this conversion require a transformation?
Thanks for your help.
Regards, Amy
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
It's an actual test subject, and I am not sure how the label was generated (someone else did it) but it looks good (matches up with that subject's amygdala nicely).
Amy
To use this cmd in this way, the label must have been created on the individual subject, if so, then rh_amy_aseg.mgz will be aligned with the brainmask.mgz. Which subject is this? If fsaverage, then it's mni305, which won't line up with mni152 in spm. To do this, spec $FREESURFER_HOME/average/mni152.register.dat as the registration file, and spec the mni152 brain as the template.
doug
amyr@nmr.mgh.harvard.edu wrote:
I used this command:
mri_label2vol --label rh_amy_aseg.label --temp ../mri/brainmask.mgz --o rh_amy_aseg.mgz
I don't know what registration matrix to use or how to generate one.
Amy
what as your label2vol command? specifically, you need to have the proper registration matrix, which is probably the problem. btw, you can use mri_label2vol to convert directly to nii.
doug
amyr@nmr.mgh.harvard.edu wrote:
Hi Freesurfers, I want to convert a freesurfer label (amygdala aseg) to a ROI (nii file?) that I can use (overlay) in SPM. I ran mri_label2vol and then mri_convert from .mgz to .nii However, the label looks a little off, and I am wondering if I need to do some sort of transformation since Freesurfer works with the Talairach and SPM works with the MNI. In SPM, I registered the BOLD images to the T1 structural image generated in Freesurfer (after running mri_convert .mgz to .img). Does this conversion require a transformation?
Thanks for your help.
Regards, Amy
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
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amyr＠nmr.mgh.harvard.edu -
Douglas N Greve