You can't do directly from preproc-sess, but you can do it from register-sess if you have an additional whole brain acquisition in the same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc) as long as it is whole brain. If your anatomical was acquired in the same session, then it is even easier because you can run register-sess with the -init-header option (instead of using fsl or spm). This assumes that the subject did not move more than 5mm between EPI and MPRAGE (usually the case). Let me know if this works for you. doug
On 6/5/12 6:03 AM, Jörg Pfannmöller wrote: > Dear Doug, > > I am having a partial field of view and a full brain scan. How can I > integrate the results in the preproc-sess sequence in order to complete the > preprocessing correctly? > > Cheers pfannmoe > > > On Mon, 04 Jun 2012 11:42:32 -0400 > Douglas N Greve<gr...@nmr.mgh.harvard.edu> wrote: > >> You can try running register-sess outside of preproc-sess, something like >> register-sess -s session -fsd bold -per-run -init-spm >> >> before you do that, you need to have spm5 and matlab, and change your >> matlab/startup.m to add the spm5 path >> path(path,'/usr/pubsw/common/spm/spm5'); >> >> doug >> >> ps. Is this whole brain coverage or are you chopping off some of the brain >> >> >> On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote: >>> Dear Doug, >>> >>> indeed the initialization fails. I was able to initiate bbregister >>> manually, giving a good registration result. Can you give me a hint how to >>> modify the registration and keeping the preproc-sess stream intact? >>> >>> Cheers >>> >>> pfannmoe >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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
