Hi Doug, You are absolutely right - I should have noticed the T1 warning in the bbregister logs. I guess funny things can happen when scanning with a short (1.15 sec) TR without fat suppression (also this was Trio before the Tim upgrade and multichannel arrays).
We tried bbregister with t1 weighting and indeed it works much better. However, to change only parameter at a time, we would prefer to run the version 5.1 analysis using the old manual register.dat. The next question is how do we do that exactly. As you suggest, we will (inside the bold directory, not inside the individual run directories) cp register.dat register.dof6.dat ... but then how should our preproc-sess command look like in order to avoid re-registering the data and overwriting our registration file? Would this simply be a matter of adding -noreg, such as: preproc-sess -s avml07 -fwhm 5 -surface fsaverage lhrh -per-session -sliceorder siemens -force -fsd bold -noreg -Tommi > wow, that's interesting. Your data is actually T1 weighted! There are a > couple of things you can do. First, you can copy your register.dat over > the register.dof6.dat. An alternative is to run register-sess > (bbregister) with t1 weighting. You can do this by creating a file with > the line "--t1" in it (no quotes) and passing that file to register-sess > with "-bbr-xopts yourfile". > > doug > > r...@nmr.mgh.harvard.edu wrote: >> Hi Doug, >> >> We have an old EPI data set where automatic (preproc-sess) or bbregister >> with any init type give a bad result. Hence, we are attempting to use a >> manual register.dat file instead. However, we must be doing something >> wrong, because changing preproc-sess to use our manual register.dat >> (done >> a couple of years ago) seems to have no effect. I suspect our >> preproc-sess >> options as not set up correctly. Our goal is to present the results on >> fsaverage surface. >> >> Our preproc-sess command line is as follows: >> >> preproc-sess -s avml07 -fwhm 5 -surface fsaverage lhrh -per-session >> -sliceorder siemens -force -fsd bold -noreg -regfile bold/register.dat >> >> The whole analysis script is at >> >> /space/adapt/1/users/tapsya/project_AVISI_avml07/avml07/Analysis_avml07_fsaverage.csh >> >> FS version = 5.1 >> machine = adapt (analysis running on cluster) >> setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs/ >> individual subject = avml07 >> surface analysis lhrh, results to be presented on fsaverage surface >> Total of 3 runs per analysis (each with different number of TRs) >> Total of categories in mkanalysis-sess = 18 (9 main plus 9 rare target) >> FIR analysis >> >> Thank you for the advice in advance! >> >> Bests, >> >> Tommi >> >> >> --- >> Tommi Raij, MD, PhD >> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >> Bldg 149, 13th St >> Charlestown, MA 02129 >> U.S.A. >> _______________________________________________ >> 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.
