_resampled and _FLIRT. In the above image rfMRI_REST1_LR.nii.gz is the original image, rfMRI_REST1_LR_resampled is from FSLEyes resample tool and rfMRI_REST1_LR_FLIRT is from FLIRT. The resampling is done based on ttpl-MNI152NLin6Asym_res-02_desc-brain_T1w.nii.gz.
Configuration for BOLD nifti original to be resampled in MNI space
So here are my some questions.
Here the resampling is just putting your original image in the grid of the MNI image, without doing any registration (linear or non linear) between the two images.
Depending on how you call FLIRT, there would be some minimisation run to register the two images together and you would get a different result than the Resampling from FSLeyes and thus a different image with slight different in size. If no registration is done by you FLIRT call, it may be that the interpolation method used for resampling is different between FLIRT and Resample and you would also get a slightly different image with the two methods and thus again a difference in size.
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