Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more.
--Lilla
On Sun, 16 Oct 2011, Joana Braga Pereira wrote:
Dear Lilla and Ed,
Thanks a lot for your suggestions, they were really really helpful!
I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools..
I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses.
Thanks a lot for your valuable help!
Joana
2011/10/15 Ed Gronenschild <ed.gronenschild@np.unimaas.nl>
Dear Joana,
Two things:
1.
You should be very careful to use fslswapdim since it may result
in an unintended left-right flipping. It's better to use fslreorient2std.
2.
The tool dt-recon computes the coregistration of the lowb volume to
the anatomical volume, see register.dat.
You can then use the following to coregister FA:
mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz
where "subject" is the output folder generated by the recon-all command.
You should not forget to set the global variable SUBJECTS_DIR
Cheers,
Ed
On 14 Oct, 2011, at 18:00, freesurfer-request@nmr.mgh.harvard.edu wrote:
Dear Bruce and Anastasia,
Thanks for the quick reply!
I tried the bbregister as you suggested but when i visualize the target and
dti image they don't look registered at all.
This is the comand i used:
bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg
/home/joana/FA/CN01/register.dat --init-fsl --dti --template-out
/home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx
I tried to use the bbregister tools to align them but I didn't get very
far...
Did i miss something?
I read in another mail something about using the register.dat created in
bbregister and do mri_label2vol but i'm not sure how to do it.
Thanks,
Joana
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