Motion correction using fsl

I’m trying to motion correct some fmri data but I have a conceptual problem with fsl motion correction part.
it motion corrects each run individually to the middle image of that specific run, and the same operation for other runs.
suppose that I don’t have T1 images and I don’t want to register my functional images to mni template, my problem is why fsl doesn’t have any option to register whole images of all runs to the middle image of the first run?
because spm has somehow (but first image of the first run) this option and I have better result of clustering using the data preprocessed by spm than fsl.

best regard

FSL has an option for an alternative reference image, in the pre-stats tab. You could use your prefered volume there, and I think it will do what you desire. If you have multiple runs, you can use the same alternative reference image for all of them.

Alternatively, you can write an email to the FSL mailing list:

FSL experts will be able to answer you there in detail (Sorry I do not know this detail in particular).


@dowdlelt @Fidel thank you!

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