Dear Doug, I have tested the various options of register-sess. The result was a succesful registration of the functional to the anatomical image. This registration with register-sess is performed after preproc-sess failed to achieve a proper registration. The register.dof6.dat file is updated by register-sess. I would like to ask a last thing just in order to make it definite. Can I now use those data for example with selxavg3-sess in order to compute the activated areas for this subject?
Greets pfannmoe On Tue, 05 Jun 2012 18:30:42 -0400 Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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 -- Jörg Pfannmöller <pfannmo...@uni-greifswald.de> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
