Hi Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug
Lilla Zollei wrote:
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:
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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