Hi,

Do step 2 but also save the transformation matrix using the -omat option.

Then do step 2 but using "-applyxfm -init blahblah" where "blahblah" should be replaced with the name of the matrix that you saved in step 1.

This will then figure out how to register a single 3D example image from the 4D to the 3D one (step 2) and then apply this same transform to all the timepoints (step 1).

All the best,

Mark

On 31 May 2018, at 21:11, Raphael F.C. <[log in to unmask]> wrote:

Dear experts, 

I am trying to register a functional 4D image to a structural 3D one. And I also want to resample the 4D image to the resolution and bounding box of the 3D image.

Is there a straightforward way to do this?

I have tried the following:

1) flirt -in 4Dimg.nii.gz -ref 3Dimg.nii.gz -out NewImg.nii.gz -applyxfm

It does resample all the volumes of the 4D image, but it translates the image to the corner of the bounding box.

2) flirt -in 4Dimg.nii.gz -ref 3Dimg.nii.gz -out NewImg.nii.gz

Then it does what I want but only for the first volume of the 4D file.

Thank you!

--

Raphael F. Casseb

Medical Physicist, Ph.D.

Seaman Family MR Research Center - University of Calgary

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