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
tapsya@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
raij@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 raij@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 greve@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 greve@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