fMRI realignment with fsl

I’m teryig to use fsl to realign my fmri to my gray matter mask. I used both flirt and feat. my out put is perfectly aligned but it is 3d and fsl removes the its timeseries, any idea how can I fix that?
thanks in advance


Can you list the steps and commands you used for these steps?


thanks for responding,
I used FSL GUI, to analyze withh FLIRT, I put my T1W image as refrence and my blod image as input.
to analyze with FEAT, I put the status as preprocessing an filled all of the steps parameters as min or zero(because my data is preprocessed just not aligned).
the output is 3D.

Usually to make these transformations, one would start by registering the BOLD ref image (not the entire timeseries) to the anatomical image, and then apply the resulting transformation to the whole BOLD image.

Interesting, and how should apply the transformation?
I used SPM and it worked well.

You can use flirt, it just may be simpler to do it on command line vs GUI. You can save the transformation from your BOLD ref → anat transform with the --omat argument, and then specify that output as the --init for your BOLD timeseries registration.

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