That should work, but it should not register anyway (unless the raw data or template change). doug
r...@nmr.mgh.harvard.edu wrote: > 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 >> >> >> > > > -- 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.
