Hi - yes, I think this sounds reasonable and should be robust and  
accurate.
Cheers.



On 14 Dec 2007, at 02:23, David Gutman wrote:

> I've experimented with Freesurfer in the past, but it's not  
> currently installed on my cluster after the latest upgrade.
>
> I was thinking of a potential low-tech solution if there's no  
> obvious way to directly transform an SPM Structural--> Standard  
> Affine Matrix to an FSL friendly version.
>
> If instead of registering my structural/T1 image to the standard  
> avg152T1 using FLIRT, I could instead register my structural T1 to  
> that same subject's brain affine transformed to standard space in  
> SPM.   Since the math should be exactly the same, and if I am using  
> the same interpolation methods (nearest neighbor or linear), same  
> DOF, and presumably the same cost function ( I have to check if this  
> can be specified with the spm function), then I should at least in  
> theory be ensuring my individual subjects are in the same "standard  
> space" as any SPM based results we generate from our other analyses.
>
> Does this sound reasonable?
>
>
> DAG
>
>
>
>
> On Dec 12, 2007 10:03 PM, Doug Greve <[log in to unmask]>  
> wrote:
> 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
> [log in to unmask]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
> -- 
> David A Gutman, M.D. Ph.D.
> Department of Psychiatry & Behavioral Sciences
> Emory University School of Medicine


---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------