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>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 > > 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 > > > 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. > >
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