How does it look in tkmedit? On 04/23/2012 12:20 PM, Long wrote: > Hi Douglas, > > I tried to do spatial normalization for volume data, all steps are > following: > > 1) bbregister --mov fsubj01_rest_res_co_001.hdr --bold --s subj01 > --init-fsl --reg bb_register.dat > > I checked the result by tkregister2, it looked good. > > 2) mris_preproc --target fsaverage --hemi lh --iv fsubj01_001.hdr > bb_register.dat --projfrac 0.5 --out lh.zmap.mgh > > 3) mri_surf2vol --surfval lh.zmap.mgh --hemi lh --identity fsaverage > --outvol subj01_001.nii.gz --projfrac 0.5 --fillribbon --template > wfrest_res_co_001.hdr > > However, the output file subj01_001.nii.gz showed wrong orientation > when viewing in MRIcron, the image looked rotated. Could you please > help with it? > > Best, > Xiangyu > > On Mon, Apr 23, 2012 at 4:31 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Hi Xiangyu, just add --identity fsaverage to the surf2vol > command line > doug > > > On 04/19/2012 05:57 PM, Long wrote: > > Hi all, > > > > I had a question when convert a surface to volume space. > > > > First, I converted a volume nifti data to fsaverage: > > > > mris_preproc --target fsaverage --hemi lh --iv data.nii > > bb_register.dat --out data.lh.mgh > > > > Then, I want to convert the data.lh.mgh to volume space, I tried > > mri_surf2vol, however, it needs register.dat. As I understood, the > > data.lh.mgh was already registered to fsaverage surface, so how > can I > > get the required register.dat file? Thank you for your attention. > > > > Best, > > Xiangyu > > > > > > _______________________________________________ > > 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> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > >
-- 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
