First, make sure that the volume you created is in register with the template functional. Eg,
tkmedit -f f.nii -ov f_LH12.mgz where f.nii is the functional that f_LH12.mgz was derived from. Once that is correct, run bbregister with the actual subject as the target (not fsaverage), spec the --mov as f.nii, and use --init-fsl instead of --init-header The vol2surf cmd is correct, though it will sample it on the subject's surface (not that of fsaverage; you can change this with --trgsubject). The tksurfer cmd is correct, just make sure to use the correct subject. doug Jason Connolly wrote: > > Dear freesurfer experts, > > I have used the mri.vol and mri.analyzehdr.vol fields to encode my > coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz). > > I then brought these data into freesurfer using the following: > > > bbregister --s fsaverage --mov > /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg > register12.dat --bold --init-header —t2 > > mri_vol2surf --mov > /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg > /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi > lh --surf white --o > /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh > > tksurfer fsaverage lh sphere --overlay > /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh > > However, I do not see anything on the sphere (or fsaverage for that > matter) … > > Can you provide any hints? > > The phase values are normalized and range from 4 – 5 and I have > converted to RAS space properly (I hope) … > > Any tips would be a big help! > > Best wishes, > > Jason. > > ------------------------------------------------------------------------ > > _______________________________________________ > 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.
