Thanks Doug! It worked!
Joana
2011/10/17 Douglas N Greve gr...@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
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:
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
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
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 gr...@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
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
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
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
Hi Joana,
You should use the lowb volume as the moving volume for the registration
and then apply the output registration matrix to your FA volume. You can
also add the --o flag to your below command so that the resampled and
registered volume gets written out at the end. You would want that
Dear FreeSurfers,
I'm trying to coregister FA images pre-processed with FSL to Freesurfer,
however i'm having a few problems and was wondering if someone could help me
out.
These are the steps that i carried out:
mri_convert subj_01/mri/brain.mgz brain.nii.gz
fslswapdim brain.nii.gz x z -y
Hi Joana - You can try our in-house tool for within-subject registration,
bbregister, with the --dti option.
a.y
On Thu, 13 Oct 2011, Joana Braga Pereira wrote:
Dear FreeSurfers,
I'm trying to coregister FA images pre-processed with FSL to Freesurfer,
however i'm having a few problems and
Hi Joana,
try bbregister.
cheers
Bruce
On Thu, 13 Oct 2011, Joana Braga Pereira wrote:
Dear FreeSurfers,
I'm trying to coregister FA images pre-processed with FSL to Freesurfer,
however i'm having a few problems and was wondering if someone could help me
out.
These are the steps that i
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