Hi all, If I were to perform a surface-based analysis, resampling to spherical space, and I did not want to smooth in the volume, would I need to preprocess my data again without smoothing or could I just specify the motion corrected volume in in a new analysis. I think the answer is: I could just specify the motion corrected volume, however, since the global mean for intensity normalization is calculated at the end of preprocessing after smoothing and exists in the fmcsm.meanval file, will there be a problem with the inorm in later stages, will it be performed etc. if I just specify the fmc volume in a new analysis? Thanks, Cameron
Yes, you just spec the motion corrected volume when you make a new analysis. You will need to re-run inorm, but you can do this outside of preproc with
inorm-sess -funcstem fmc ...
Cameron Ellis wrote:
Hi all, If I were to perform a surface-based analysis, resampling to spherical space, and I did not want to smooth in the volume, would I need to preprocess my data again without smoothing or could I just specify the motion corrected volume in in a new analysis. I think the answer is: I could just specify the motion corrected volume, however, since the global mean for intensity normalization is calculated at the end of preprocessing after smoothing and exists in the fmcsm.meanval file, will there be a problem with the inorm in later stages, will it be performed etc. if I just specify the fmc volume in a new analysis? Thanks, Cameron _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, related to this topic, would I have to register my functionals twice if I have resampled to spherical and talairach space for two separate analyses? Register once using the motion corrected volume for spherical and once using the motion corrected smoothed volume for talairach? Cameron
Yes, you just spec the motion corrected volume when you make a new analysis. You will need to re-run inorm, but you can do this outside of preproc with
inorm-sess -funcstem fmc ...
Cameron Ellis wrote:
Hi all, If I were to perform a surface-based analysis, resampling to spherical space, and I did not want to smooth in the volume, would I need to preprocess my data again without smoothing or could I just specify the motion corrected volume in in a new analysis. I think the answer is: I could just specify the motion corrected volume, however, since the global mean for intensity normalization is calculated at the end of preprocessing after smoothing and exists in the fmcsm.meanval file, will there be a problem with the inorm in later stages, will it be performed etc. if I just specify the fmc volume in a new analysis? Thanks, Cameron _______________________________________________ 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
No, only one template is used for all.
Cameron Ellis wrote:
Hi, related to this topic, would I have to register my functionals twice if I have resampled to spherical and talairach space for two separate analyses? Register once using the motion corrected volume for spherical and once using the motion corrected smoothed volume for talairach? Cameron
Yes, you just spec the motion corrected volume when you make a new analysis. You will need to re-run inorm, but you can do this outside of preproc with
inorm-sess -funcstem fmc ...
Cameron Ellis wrote:
Hi all, If I were to perform a surface-based analysis, resampling to spherical space, and I did not want to smooth in the volume, would I need to preprocess my data again without smoothing or could I just specify the motion corrected volume in in a new analysis. I think the answer is: I could just specify the motion corrected volume, however, since the global mean for intensity normalization is calculated at the end of preprocessing after smoothing and exists in the fmcsm.meanval file, will there be a problem with the inorm in later stages, will it be performed etc. if I just specify the fmc volume in a new analysis? Thanks, Cameron _______________________________________________ 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
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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Cameron Ellis -
Doug Greve