External Email - Use Caution
Hello,
please, could you help me with this case? What am I doing wrong?
Thanks a lot
________________________________
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.
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.
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"
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
________________________________
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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