Thanks Sebastian and Doug, that clears everything up. -Clark
On Sep 26, 2011, at 11:27 AM, Douglas N Greve wrote: > > > Clark Fisher wrote: >> Hi Doug, >> >> Thanks for pointing me back to that; I had forgotten how much depth it >> goes into! I have 2 remaining questions: >> >> 1) Why is the tkr vox2ras transform sometimes dramatically different >> from the one in the volume header? For instance, in one of the >> functional volumes I'm talking about, "mri_info --vox2ras" gives: >> >> -3.42822 0.21499 0.15398 101.74103 >> -0.24476 -3.27187 -1.19314 135.02863 >> 0.06182 -1.03201 3.81480 -30.98481 >> 0.00000 0.00000 0.00000 1.00000 >> >> while "mri_info --vox2ras-tkr" gives: >> >> -3.43750 0.00000 0.00000 110.00000 >> 0.00000 0.00000 4.00000 -70.00000 >> 0.00000 -3.43750 0.00000 110.00000 >> 0.00000 0.00000 0.00000 1.00000 >> >> I would understand if the tkr-vox2ras only did flips and 90º rotations >> to put the data as close to RAS format as possible without having to >> interpolate, but the orientations produced by those 2 transformations >> are very different, with the rows and the slices essentially switched. >> I would guess that it has something to do with this explanation from >> Slide 5, but I don't quite understand it: >> >> "Field-of-View based – only depends on the identity of columns, rows, >> and slices, the number of voxels in each dimension, and their sizes. >> Unrelated to the “true” geometry but is an RAS coordinate system when >> the volume is “Coronally” sliced, which is the based “conformed” >> orientation in FreeSurfer." >> >> Any additional clarity you could provide would be appreciated. > The tkr vox2ras is not related to RAS/LIA/etc and you should not attempt > to understand it using these terms. It will always have the same pattern > of zeros and non-zeros regardless of the true geometry. Given the number > of voxels in each dimension and the voxel size in each dimension, one > can write down the tkr vox2ras without knowing anything else above the > volume. This unfortunate situation is historical. The true geometry as > it relates to the tkr geometry ends up being embedded in the > registration matrix. In the end, neither the tkr vox2ras nor the > registration matrix are interpretable by themselves (but together they are). >> >> 2) In Freesurfer XYZ space, why are the volumes centered at (# of >> voxels)/2? I would think that centering at ((# of voxels) + 1) /2 >> would put the true center of the volume on the origin. > You are correct. This is another unfortunate accident of history. > doug >> >> Thanks again, >> Clark >> >> On Sep 20, 2011, at 2:14 PM, Douglas N Greve wrote: >> >>> Hi Clark, have you looked at this documentation yet? >>> http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.ppt >>> >>> <http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.ppt> >>> doug >>> Clark Fisher wrote: >>>> Hello, >>>> >>>> I was wondering what orientation conventions are used when >>>> calculating the affine transformation matrix in register.dat. For >>>> an example, I'll use the data from subject 101 of the fsfast >>>> tutorial. According to mri_info, the functional volume is in LPS >>>> orientation, and the processed anatomical volume (T1.mgz) is in LIA >>>> orientation. Does the matrix in register.dat convert from the >>>> functional LPS orientation to the anatomical LIA orientation, or >>>> does the matrix assume these volumes are already transformed in some >>>> other way? >>>> >>>> Thanks, >>>> Clark >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> [email protected] >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> [email protected] >>> 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. >>> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > 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 > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
