Dear freesurfer experts, I have a question regarding how to incorporating bbregister coregistered mean image into the SPM batch.
After realignment step, I convert the mean functional image from the analyze format to nii format (to avoid flipping brain using bbregister)
Then, I use bbregister to co-register the mean functional image to subjects' surfaces using following command
bbregister -- s subject_name_freesurfer -- mov mean.nii --init-spm -- bold --reg register.dat -- spm-nii
After this step, is the mean.nii the coregistered image already? If it is, in SPM, shall I skip the coregistration and segmentation step? If I do skip them, in the Normalization step, is the following correct?
source image: mean.nii that has been coregistered in bbregister
image to write: (Dependency) realigned session1 and realigned session2
template image: EPI
Thank you very much for your help.
Helen
Hi Helen, it is not aligned. You will need to apply the registration with mri_vol2vol or use the --o option to output a volume. I did not follow how you are trying to incorporate this into the SPM pipeline. Also note that if you are using SPM8, make sure to added --spm-nii or else you will get LR reversals. doug
On 02/28/2013 04:24 PM, Chen, Xiaoyan wrote:
Dear freesurfer experts, I have a question regarding how to incorporating bbregister coregistered mean image into the SPM batch.
After realignment step, I convert the mean functional image from the analyze format to nii format (to avoid flipping brain using bbregister)
Then, I use bbregister to co-register the mean functional image to subjects' surfaces using following command
bbregister -- s subject_name_freesurfer -- mov mean.nii --init-spm -- bold --reg register.dat -- spm-nii
After this step, is the mean.nii the coregistered image already? If it is, in SPM, shall I skip the coregistration and segmentation step? If I do skip them, in the Normalization step, is the following correct?
source image: mean.nii that has been coregistered in bbregister
image to write: (Dependency) realigned session1 and realigned session2
template image: EPI
Thank you very much for your help.
Helen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Doug, Do you mean that the functional file mean.nii is not aligned with the structural data? I know that -- o means resample mov and save as outvol. Why do you need to resample the mean.nii? To align with structural data in freesurfer? If you do that, will the outvol be able to later be incorporated into SPM since it's not in the same dimension as it originally was? Thank you very much.
I added -- spm-nii previously. Does this works?
bbregister -- s subject_name_freesurfer -- mov mean.nii --init-spm -- bold --reg register.dat -- spm-nii -- o mean_new.nii
Helen
On Feb 28, 2013, at 6:29 PM, Douglas N Greve wrote:
Hi Helen, it is not aligned. You will need to apply the registration with mri_vol2vol or use the --o option to output a volume. I did not follow how you are trying to incorporate this into the SPM pipeline. Also note that if you are using SPM8, make sure to added --spm-nii or else you will get LR reversals. doug
On 02/28/2013 04:24 PM, Chen, Xiaoyan wrote:
Dear freesurfer experts, I have a question regarding how to incorporating bbregister coregistered mean image into the SPM batch.
After realignment step, I convert the mean functional image from the analyze format to nii format (to avoid flipping brain using bbregister)
Then, I use bbregister to co-register the mean functional image to subjects' surfaces using following command
bbregister -- s subject_name_freesurfer -- mov mean.nii --init-spm -- bold --reg register.dat -- spm-nii
After this step, is the mean.nii the coregistered image already? If it is, in SPM, shall I skip the coregistration and segmentation step? If I do skip them, in the Normalization step, is the following correct?
source image: mean.nii that has been coregistered in bbregister
image to write: (Dependency) realigned session1 and realigned session2
template image: EPI
Thank you very much for your help.
Helen
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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Chen, Xiaoyan -
Douglas N Greve