If the head has not moved, then they will share a scanner RAS, ie, a given scanner RAS will be at the same place in the head in the two scans, though they will map to different col,row,slice in their respective volumes. If the head has moved, then you will need to perform a registration to get them aligned.
On 11/11/2016 04:17 PM, Krieger, Donald N. wrote: > Thanks for getting back, Doug. > I understand - but if there are two scans, aren't there two scanner RAS's > since the head presumably moved at least a little from one to the other or > the scans could have been done on different scanners? > > Don > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, November 11, 2016 3:22 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple > input scans > > -tkr2scanner gives the transform that takes "tkregister RAS" and > converts it to scanner RAS. "tkregisterRAS" is the RAS system used by > surfaces (it, a vertex xyz is in tkregisterRAS). See > http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems > > > > On 11/10/2016 09:33 PM, Krieger, Donald N. wrote: >> If I run recon-all with both a T1 and a T2 scan and switch t2pial, >> does mri_info –tkr2scanner give me the transform to the T1 scanner >> frame of reference? >> >> And if I run recon-all with many T1’s , what does mri_info >> –tkr2scanner give me then? >> >> Thanks - Don >> >> >> >> _______________________________________________ >> 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 > > > 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
