If you have freesurfer installed, you can try using tkregister2. If
you've coregistered your dti to your desired space (without reslicing),
then you can do something like:
tkregister2 --mov dti.nii--targ yourtemplate.nii --regheader --reg
junk.dat --fslregout flirt.mat
This will bring up the graphical interface which will allow you to view
(and perhaps modify) the registration. If the registration does not look
good there, then flirt.mat will not be correct. When you hit "Save Reg"
it will write out the flirt.mat matrix.
The only other thing to consider is your file format. If you are using
ANALYZE, then this stands a good chance of failing because FSL may load
your image in diffrently depending upon the format and the handedness.
This means tkregister2 has to account for this, and it can with nifti,
but it just has to guess with ANALYZE.
Anyway, if that works and you want to run it without the interface, you
can add --noedit to the cmd line.
good luck
doug
David Gutman wrote:
> I saw this mentioned a long time ago on the list serve, but was
> wondering if anyone has a script/easy solution they could share.
>
> Basically several people in my lab use SPM for parts of their data
> analysis, in particular using the spm_preproc() function to normalize
> their T1 images into standard space.
>
> I've been relying solely on FLIRT for all my spatial normalization,
> but there are sometimes small (and sometimes bigger) differences in
> the registration quality produced by FLIRT vs SPM. Since double
> checking registration is both time consuming and/or frustrating; also
> as we share results it would be nice if all of our results were in
> exactly the same space! I was thinking I could use the Affine
> transformation matrix outputted by SPM and directly supply it to FLIRT
> and/or use it for DTI analysis.
>
> As I quickly learned, doing so places the " transformed brain" outside
> of the actual view. Poking around a little bit more, it appears there
> are a number of significant differences in what information FSL and
> SPM puts into the 4x4 matrix, differences in the size of the bounding
> boxes, as well as using different numbering conventions and/or
> different assumptions about the origin.
>
> Is there any relatively straightforward solution to this problem? I'd
> rather not reinvent the wheel if I don't have to.
>
>
> DAG
>
>
>
> --
> David A Gutman, M.D. Ph.D.
> Department of Psychiatry & Behavioral Sciences
> Emory University School of Medicine
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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