Hi Tapsya, If you want to supply a registration to bbregister, then use --init-reg (and don't use --init-fsl). The xopts should give you the same result as the first command. doug
tap...@nmr.mgh.harvard.edu wrote: > Hi Doug, > > As mentioned below (by Dr. Tommi), bbregister with the flag --t1 does > provide better results. i.e. > > >>> bbregister --init-fsl --s avml07 --bold --mov bold/template.nii.gz --reg >>> > bold/register.dof6.dat --init-reg-out bold/init.register.dof6.dat --t1 > > > However, supplying register.dat (from old manual) to the bbregister > command did not work for me, > > >>> bbregister --init-fsl --s avml07 --bold --mov bold/template.nii.gz --reg >>> > bold/register.dof6.dat --init-reg-out bold/register.dat --t1 > > Here the registration was completely off. Is there any reason why > providing old register.dat did not work? > > I also tried the program register-sess. i.e. > > >>> register-sess -s avml07_cpy -d >>> > /space/adapt/1/users/tapsya/project_AVISI_avml07/ -per-session -bbr-xopts > xopts -regfile registration.dof6.dat -fsd bold > > where xopts is a text file whose contents are --t1. Here the results were > pretty much similar to the first bbregister command above. Am I supposed > to see any difference between register-sess and bbregister (first > bbregister command above)? > > Please do let me know if I am doing wrong somewhere. > > Thanks for helping in advance. > > Wishes, > Tapsya > > > >> 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 >> >> >> >> > > > > > > > -- 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.
