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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.