You don't need to do the bbregister or tkregister steps if the FS results are based on the T1.nii image as input. You can just use mri_vol2vol with --regheader instead of --reg t1.reg.dat (but the results should be about the same).
For the problem, does aparc+aseg show up properly on the T1.nii? what is your freeview command line? On 02/14/2017 01:54 PM, John Anderson wrote: > Thank you very much! > Kindly, I have one follow up question: > I have VOI 20X20X20 mm have been created during an MR spectroscopy > session. This VOI was placed in specific loacation on the T1 image. I > have created this VOI using the command "mri_volsynth" and I want to > move it from native space (T1) to Freesurfer space (e.g. wmparc.mgz) > so I can generrat somestatistics using the command "mri_segstats". > I ran the following commands: > bbregister --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj > tkregister2 --mov VOI.nii --int T1.nii t1.reg.dat --reg VOI.reg.dat > --noedit --subject subj > mri_vol2vol --mov VOI.nii --reg t1.reg.dat --fstarg --interp nearest > --o VOI.anat.nii > Are these stpes correct? > When I open T1.nii and the VOI.nii in freeview, I can see the VOI in > it is correct position. But when I open "wmparc.mgz" and > "VOI.anat.nii" then VOI is not showing in the correct position. I > suspet that I am doing something wrong in the previous steps and I > highly appreciate any feedback! > Best, > John > For version 6, it should not matter. > *Sent:* Friday, February 10, 2017 at 4:03 PM > *From:* "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > *To:* "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] bbregister > Hi John > > one of the many nice things about bbregister is that it is quite > resistant to non-brain tissue, since it's just trying to place the > gray/white (and optionally the pial surface) at a reasonable spot in the > volume. I guess it might make the initialization less robust, not > sure, but > I expect it works pretty well without doing brain extraction > > cheers > Bruce > > On Fri, 10 Feb 2017, John Anderson wrote: > > > Hi FS experts, > > I want to register T1 image to its freesurfer space (i.e. > wmparc.mgz) using > > the command > > bbregister --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj > > > > do I need to apply brain extraction tools before this step or bb > register > > can accept non-brain extracted images? > > > > Best, > > John > > > >_______________________________________________ > 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. > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
