Does anyone know? below is my original message again:
Thanks!
Hi FSL experts,
I seem to run into issues with slice timing correction. I scanned my study with a multi-band factor of 2, and TR of 2s. I then ran slice-timing correction and MELODIC (all within FEAT). I did no smoothing, just motion correction. For the slice timing correction, I used a timing file per the recommendation when using multiband. To my understanding, I should provide the time by which I want to shift the data in TR units. For example, the first slice (or group of slices in multiband), should have the value of 0.5, because I should have a 0.5 TR shift forward in time.
When I did that, the ICA looked like I have slice effects, they appeared in all of the components
(see an image taken from MELODIC's report: https://drive.google.com/file/d/1QGLtmbovSoJv6vL7xVklQ6vWnEbBqQ1i/view?usp=sharing ). It suggests to me that something is wrong with my slice-timing correction, but I have no idea what I did wrong. Importantly, I don't see this artifact, and I get a more reasonable number of components (~40 instead of ~160), if I run MELODIC without slice-timing correction. The Excel file I attach (https://drive.google.com/file/d/1jpm1Iqf9jJkgYUSyTSgGgMwhfvbR_GdF/view?usp=sharing , sorry for the links, files were too big to upload) has the conversion from the timing I have of the slices to the shift in TR unites (sorry for the low tech, the relevant columns are A and E, I think it's self-explanatory).
I use FSL 6.
Any ideas of what I did wrong?
I know that slice timing correction is controversial with short TRs, but I would like to use it, or at least understand the problem or how to do it correctly.
Thanks!
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