Actually, (1) should be more accurate, because bbregister uses the surface reconstruction obtained from the T1 to optimize the contrast across the gray/white boundary in the registered DWI.
However if you want to convert to the 1mm, 256^3 voxel size that was used as input to freesurfer, see mri_convert --conform. On Mon, 26 Mar 2012, Johnson wrote: > Hi > Let me re-phrase my question: > I already did registration from DWI to T1, this step is OK. > Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not the > aparc+aseg-in-rawavg file). I know I have two choices: > 1) do registration using bbregister > 2) since Freesurfer during processing have already done this step, the > transformation matrix is there somewhere, the question is where to find it? > which log or which file? this choice is better since it is more accurate. > > Thanks > JG > > On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: >> >> If you want to register your DWI to T1, you should register to >> mri/brain.mgz. You can do this with bbregister, or with any affine >> registration tool of your choice. >> >> On Mon, 26 Mar 2012, Johnson wrote: >> >> > Hi >> > I found it in a 256x256x256 space while the T1 we use is in different >> > space, I found this page on the registration step: >> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >> > I wish to know how this script work? >> > >> > mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz >> > --regheader aseg.mgz >> > >> > what is the transformation used ? >> > JG >> > >> > >> > On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: >> > > >> > > Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used >> > > as >> > > input to freesurfer. >> > > >> > > a.y >> > > >> > > On Mon, 26 Mar 2012, Johnson wrote: >> > > >> > > > Hi FS expert >> > > > I need to know the transformation matrix itself since I will do >> > > the > transformation in matlab. >> > > > I successfully transformed white matter fibers coordinates to T1 >> > > using > AIR 5.0 from LONI lab. >> > > > They provide a transformation matrix. >> > > > Now I want to transform the coordinates from T1 to Freesurfer >> > > space, so >> > > > my question is: what is the transformation matrix that relates >> > > the T1 >> > > > which FS have used for parcellation and segmentation with the > >> > > aparc+aseg.mgz file? >> > > > I searched the logs but couldn't find such matrix. >> > > > I don't want to do a registration step since it will be less >> > > accurate > than the one that was generated during the segmentation >> > > process. >> > > > Also is it just one transformation or a combination of >> > > transformations? >> > > > > thanks >> > > > > >> > > >> > > 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
