Hi - I don't think you can estimate, and apply a transform to a 4D
image simultaneously.
I think you need to do the following:
1) Register the b=0 image to the MNI template using FLIRT and save
the transformation matrix.
2) Apply this transformation matrix to the full 4D volume (using
ApplyXFM)
This will then save all of your volumes in the output.
Remember that you will have to rotate the b-vectors as well if you
want your fitted diffusion tensors to make sense.
T
On 2 Jan 2007, at 09:08, Anna Rotarska-Jagiela wrote:
> Dear FSL expersts,
> I’m trying to align my raw DTI data using FLIRT and write it out in
> Analyze
> format.
> Here is what I did: I created a single Analyze file of raw DTI data (7
> volumes, 6 directions + b0), did EPI distortion correction and
> saved it
> again as a single Analyze file. Then I opened FLIRT window,
> selected input
> image (a single Analyze EPI-corrected file with 7 volumes), named
> output
> image. I left all the other setting at default, including the
> reference
> image, i.e. MNI template. I clicked on go and checked the results
> in MRIcro.
> Here is the problem: The alignment worked fine, but the volumes got
> lost. I
> can only open the first, b0 volume. MRIcro doesn’t ask anymore
> which volume
> it should show (1 through 7) like it did with EPI-corrected image.
> It only
> recognizes the first one.
> Here is the question: What did I do wrong? How do I align all 7
> volumes and
> save them back to a single Analyze file?
> I would appreciate your help.
> Thank you.
>
> Anna
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