use bbregister, something like bbregister --s subjectname --init-fsl --t2 --mov lowb.nii --reg register.dat where lowb is the low b (usually b=0) volume from your DTI, the one that you used as the template for motion correction. doug
On 11/19/2012 10:30 AM, Bruce Fischl wrote: > Hi Longchuan > > yes, I think you can do this with tkregister2. Doug can give you the > details > Bruce > On Mon, 19 Nov 2012, Longchuan Li wrote: > >> Hi, Bruce >> >> Thank you for the information. I will re-run recon-all using "-cm" >> option to >> see if the problem will be solved. In the mean time, do you have any >> suggestions regarding finding a transformation between the mismatched >> surfaces and the volume? >> >> Thanks again. >> >> Longchuan >> >> >> ____________________________________________________________________________ >> >> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> To: Longchuan Li <leonad...@yahoo.com> >> Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu> >> Sent: Monday, November 19, 2012 8:57 AM >> Subject: Re: [Freesurfer] the positions of white/pial surfaces and the >> brain.mgz >> >> Hi Longchuan >> >> have you tried the -cm (conform to min) option in recon-all? >> >> cheers >> Bruce >> >> >> On Sun, 18 Nov >> 2012, Longchuan Li wrote: >> >> > Hi, FreeSurfer experts >> > >> > I have a question regarding coregistering white and pial surfaces >> with the >> brain.mgz and would appreciate your help on this. I >> > am working on non-human primates and noticed that my white and pial >> surfaces do not have identical positions as brain.mgz. For >> > example, when I used "mris_fill" to write white and pial surfaces into >> volume files, they do not have same sto_xyz and qto_xyz >> > values as these in the brain.mgz. This is not the case for human >> data. So >> my questions are: >> > >> > (1) how could I find a transformation matrix between the two, so >> that when >> I am using surface-based tractography in the future, >> > the program can find the correspondence between the points on the >> surfaces >> and those in the volumetric diffusion MRI data? >> > >> > (2) How in the future, can I avoid such misregistrations in generating >> non-human primate surface files in FreeSurfer? >> > >> > Thank you very much in advance! >> > >> > Longchuan >> > >> > >> >> >> 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: 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
