Hi Elisa, sorry about that. Yes, use the $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat instead. doug
Elisa Golfinopoulos wrote: > Hi Doug, > > Thanks for responding to my inquiry. My version of Freesurfer (v.5) > does not contain > > mni152.mni305.cor.subfov2.dat > > in the average folder. I did notice that the most recent version of > freesurfer has the reg.2mm.mni152.dat > > in the same folder as the subcortical mask. > > Thanks so much for your help! > Take good care. > Elisa > > > On Tue, Jun 7, 2011 at 6:15 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Eventhough they are both in "MNI" space, there is still a > registration that has to be applied. Try something like this: > > > mri_vol2vol --mov > $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz \ > --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ > --reg $FREESURFER_HOME/average/mni152.mni305.cor.subfov2.dat \ > --o ./subcort.mask152.nii > > Elisa Golfinopoulos wrote: > > Hi, > > I would like to normalize the subcort.mask.mgz to MNI152 > space. I have attempted to use the command: > > mri_vol2vol --mov $FREESURFER_HOME/subjects/ > fsaverage/mri.2mm/subcort.mask.mgz > --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz > --o ./subcort.mask152.nii > --reg $FREESURFER_HOME/average/mni152.register.dat > > but when I check the registration with the MNI152 template I > find that the 152 normalized subcortical mask does not align > with the template. The problem is somewhat resolved when I > specify a 180 degree rotation along the x axis (though there > still appears to be some translation error). However, I feel > uncomfortable using rotations/translations without > understanding why the registration is incorrect in the first > place. > > In fact, this problem is making me question whether a > transformation is really necessary since, technically, both > the mask and the target are in MNI space and the registration > of the original MNI 305 subcortical mask with the MNI152 > template looks more accurate than the 152 normalized mask. Any > help that you can offer would be greatly appreciated. > > Cheers, > Elisa > > > -- > Elisa Golfinopoulos > Speech Laboratory > Cognitive and Neural Systems > Boston University > Phone: 617.353.6181 <tel:617.353.6181> <tel:617.353.6181 > <tel:617.353.6181>> > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > -- > Elisa Golfinopoulos > Speech Laboratory > Cognitive and Neural Systems > Boston University > Phone: 617.353.6181 <tel:617.353.6181> > -- 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
