Hi Jason you can't get all the voxels onto the surface, as the surface is a 2D sheet cutting through a 3D volume. This is actually one of the big advantages of surface-based analysis as you avoid most of the regions that shouldn't have signal (e.g. ventricles, white matter, etc...). That said, there are some options in mri_vol2surf you can explore for changing the way you project from volume to surface. Check out Doug's excellent help.
cheers Bruce On Thu, 10 Feb 2011, Jason Connolly wrote: > Dear Doug, > > Thank you! I was able to display on the freesurfer surface from a matlab > array to surface pipeline. > > However, only a portion of my voxels showed up on the surface, presumable > owing that the others fall in the white matter ... > > My question is: is there any way to override this so that all the voxels are > 'forced' to display on the surface? > > Many thanks, > > Jason. > > >> -----Original Message----- >> From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] >> Sent: 09 February 2011 16:42 >> To: Jason Connolly >> Cc: 'freesurfer@nmr.mgh.harvard.edu' >> Subject: Re: [Freesurfer] phase data overlay using fsaverage >> >> 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 >> >> >> >> 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. > > > _______________________________________________ > 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
