Jiansong,
I recommend applying art_global repairs after normalization and smoothing.
Slide #4 is confusingly worded.
It's best to noise filter for bad slices using art_slice before any preprocessing.
There are two issues to consider if you want to Repair using art_global before preprocessing:
-If your volume one is corrupted by not being magnetically stablized, and realignment
will be done relative to scan 1, then you might want to fix scan 1 first before realignment.
But best practice is either to start the experiment a few scans after the scan start (so mag
stability is not an issue), or to realign with respect to the mean scan. In either case, there
is no need to repair it. (Repair will just copy the nearest good volume to that spot).
-If there were a huge glitch on a volume, then slice timing may spread it to neighboring
volumes. But I believe these errors would be caught anyway by the addmargin function
in art_global later on. So there is probably no need to do this.
In summary, there is probably no need to repair using art_global before preprocessing. There
is a warning alert next to the Repair button as a hint not to do this. That being said, I often
look at the art_global figure just as a quality check of which scans might be bad, and then
review those scans with art_movie.
Regards,
Paul
>I have one more question. That is when to repair the excessive motion?
>It is said that "A good opportunity is just before estimation." in the
>section of DETECT AND REPAIR VOLUME ARTIFACTS in the Artifact Protocol.
>My understanding is after spatial normalization and smooth.
>But in the power point Artifact Example, it is mentioned in slide #4, that
>the good place for repair is before SPM preprocessing. My understanding is
>to use SPM do realign and reslice, than apply repair.
Best Regards
Jiansong
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