Now I don't understand. Here's the situation: Someone has given me a bunch of MEG's with freesurfer runs which were run using both a T1 and a T2 scan with -T2pial . Mri_info --tkr2scanner gives the same transform for aparac+aseg.mgz, T1.mgz, and T2.mgz . I will be coregistering the MEG which comes with each T1/T2 pair . Since I'm getting the same transform from all the .mgz's, I speculated that freesurfer transformed both scans to tkr coordinates, did its thing, and then picked the T1 to provide the tkr2scanner transform. ???
Don > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Friday, November 11, 2016 4:35 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple > input > scans > > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
