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*Od:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> za uživatele Adam Rytina
<adam.ryt...@outlook.cz>
*Odesláno:* sobota 15. února 2020 19:52
*Komu:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Předmět:* Re: [Freesurfer] Apply transformation
External Email - Use Caution
Thanks, unfortunately, I am making some mistake but I don´t know where.
First of all I run autorecon1 on my anatomical T1 data (the orig.mgz
image is saved in /usr/local/freesurfer/subjects/anatomical).
Then in the /usr/local/freesurfer/data I run mri_robust register
command of the T1 and diffusion DWI data. The registration.lta file is
saved here.
Don't use robust register for this, use bbregister (but you will have to
run recon-all to completion)
Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder
/usr/local/freesurfer/data that I want to transform to the anatomical
T1 space.
Is this in the conformed space (ie, same as orig.mgz)?
In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta
registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s
anatomical --fstarg"
If you are trying to transfer it to the DTI space, then use
mri_vol2vol --lta bbr.registration.lta --targ 3D_T1_brain_mask.nii --mov
dti.nii --o f-in-anat3.nii --s anatomical --interp nearest
To sum up, I am aiming to apply a transformation matrix on the T1
anatomical brain mask and transform it to the T1 space defined by 3D
T1 image.
The problem is this command transforms orig.mgz file (a skull stripped
T1 image) instead of 3D_T1_brain_mask.nii.
Please, do you know where I make mistake?
Thanks a lot
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*Od:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> za uživatele Douglas Greve
<dgr...@mgh.harvard.edu>
*Odesláno:* sobota 15. února 2020 17:15
*Komu:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Předmět:* Re: [Freesurfer] Apply transformation
Yes, mri_vol2vol
On 2/15/20 11:07 AM, Adam Rytina wrote:
External Email - Use Caution
Hello all,
I want to apply the saved transformation (a transformation matrix 4x4
acquired by registration of an anatomical and a diffusion image) on
my input anatomical mask and change a final FOV by specifying a
diffusion reference image (its voxels size). It means to apply the
same command as the command ApplyXFM in FSL FLIRT. Does this option
exist also in Freesurfer?
Thanks a lot
Regards
Adam
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