Thank you for your advice Doug. Best wishes,
-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
