Dear Megan,
I couldn't see the movie you made but one thing to be careful about is
to use the same intensity scaling for all the images (instead of using
something based on the min/max of each individual 2D image) otherwise
some of the flickering you see might be partly artefactual.
If you were to use CheckReg (and the Browse > Save Movie option) to
create a movie, you would first use Intensity > Range > This image >
Manual or Percentile to make sure this was the case.
Best regards,
Guillaume.
On 13/07/18 23:06, Megan Finnegan wrote:
> Hello SPM Community,
>
> I am creating movies of some NIfTI files before preprocessing from EPI runs to get a better sense of my data (and because making brain movies is fun). I've noticed that many of the runs have what appears to be flickering in global signal instensity throughout the scan. This seems particularly prevalent on subjects with high motion, making me think that it is perhaps spin history artifacts, but even subjects who have very little motion have some of this flickering.
>
> I don't have a sense of what a "normal" EPI should look like and if this kind of behavior is within the bounds of acceptable or is something I should be concerned about. Any thoughts on whether this is normal, what the primary causes could be, and if this is something that can/should be minimized (and how to) in future studies would be greatly appreciated.
>
> Here is a link to one of these movies to give you a sense of what I'm talking about.
>
> heuristicwondering.com/brainsharing/brainmovie.html
>
> On this note too, I've seen labs at my campus engage in varying levels of visual inspection of data at different points along the analysis pipeline. What is your opinions on visual inspection best-practices? In particular, if you have very large studies, what are the essential images to look at to ensure things are going alright, what is optional? What is feasible?
>
> Thank you in advance!
>
> ~Meg
>
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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