Joana

2011/10/17 Douglas N Greve <greve@nmr.mgh.harvard.edu>

No, use the register.dat that you manually created as the input to bbregister with the --init-reg. You could move your register.dat to regidster.man.dat and set the output to be register.dat.

doug

Joana Braga Pereira wrote:

Hi Doug,

Thanks for the reply. I'm not sure i understand how to solve it.
Are you suggesting to re-run bbregister using the --init-reg option and the register.dat files that were previously created for the badly-registered subjects?

Joana

2011/10/17 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>

Those almost surely failed because of a bad initialization. You
can usually tell this by looking at the first value in the mincost
file. For these, the mincost is something like .9. The mincost
will be a value bet 0 and 1.1, with 0 being perfect. Looks at your
good subjects to get an idea of what range to expect for
well-registered subjects. You should be able to use the
registrations you created as input to bbregister (with the
--init-reg option), and bbregister should do fine after that.
doug

Joana Braga Pereira wrote:

Hi Doug,

I made quite a few changes, including translations and
rotations (not scaling changes), to 10 out of 24 subjects.

Here are a few of the bbregister log.files from subjects in
which the registration didn't go well.

Thanks for the help!

Joana

2011/10/17 Douglas N Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu

<mailto:greve@nmr.mgh.harvard.edu>>>

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
<mailto:ed.gronenschild@np.unimaas.nl>
<mailto:ed.gronenschild@np.unimaas.nl

<mailto: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
<mailto:freesurfer-request@nmr.mgh.harvard.edu>
<mailto:freesurfer-request@nmr.mgh.harvard.edu

<mailto: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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MGH-NMR Center
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