Re: [Freesurfer] fsaverage to mni152
Use $FREESURFER_HOME/average/mni152.register.dat and mri_vol2vol with --inv Yigal Agam wrote: > Hi, > > What's the best way to convert an fsaverage volume into an MNI152 volume > that can be viewed on top of a standard brain > (MNI152_T1_2mm_brain.nii.gz) in fslview? > > Thanks, > Yigal > ___ > 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 gr...@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
Re: [Freesurfer] fsaverage to mni152
Thanks, Doug. Also, how can this be done from an individual brain to mni152? Do I need to use fsaverage as an intermediate? Yigal Douglas N Greve wrote: > Use $FREESURFER_HOME/average/mni152.register.dat and mri_vol2vol with > --inv > > Yigal Agam wrote: >> Hi, >> >> What's the best way to convert an fsaverage volume into an MNI152 >> volume that can be viewed on top of a standard brain >> (MNI152_T1_2mm_brain.nii.gz) in fslview? >> >> Thanks, >> Yigal >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fsaverage to mni152
Nope. Try using fslregister with --dof 12 and use $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz as the --mov. doug Yigal Agam wrote: > Thanks, Doug. Also, how can this be done from an individual brain to > mni152? Do I need to use fsaverage as an intermediate? > > Yigal > > Douglas N Greve wrote: >> Use $FREESURFER_HOME/average/mni152.register.dat and mri_vol2vol with >> --inv >> >> Yigal Agam wrote: >>> Hi, >>> >>> What's the best way to convert an fsaverage volume into an MNI152 >>> volume that can be viewed on top of a standard brain >>> (MNI152_T1_2mm_brain.nii.gz) in fslview? >>> >>> Thanks, >>> Yigal >>> ___ >>> 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 gr...@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
Re: [Freesurfer] fsaverage to mni152
Hi Doug, Returning to this old thread: I'm doing what you said and getting weird results (activation not where I think it should be): mri_vol2vol --mov --targ --inv --reg $FREESURFER_HOME/average/mni152.register.dat --o --no-save-reg Can you give an example of the command you would use? Thanks, Yigal Douglas N Greve wrote: > Use $FREESURFER_HOME/average/mni152.register.dat and mri_vol2vol with > --inv > > Yigal Agam wrote: >> Hi, >> >> What's the best way to convert an fsaverage volume into an MNI152 >> volume that can be viewed on top of a standard brain >> (MNI152_T1_2mm_brain.nii.gz) in fslview? >> >> Thanks, >> Yigal >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fsaverage to mni152
That is the command that I would use. Make sure your activation map actually lines up with the MNI152 brain found in FSL. dopug Yigal Agam wrote: > Hi Doug, > > Returning to this old thread: I'm doing what you said and getting > weird results (activation not where I think it should be): > > mri_vol2vol --mov --targ --inv > --reg $FREESURFER_HOME/average/mni152.register.dat --o volume> --no-save-reg > > Can you give an example of the command you would use? > > Thanks, > Yigal > > > > Douglas N Greve wrote: >> Use $FREESURFER_HOME/average/mni152.register.dat and mri_vol2vol with >> --inv >> >> Yigal Agam wrote: >>> Hi, >>> >>> What's the best way to convert an fsaverage volume into an MNI152 >>> volume that can be viewed on top of a standard brain >>> (MNI152_T1_2mm_brain.nii.gz) in fslview? >>> >>> Thanks, >>> Yigal >>> ___ >>> 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 gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
