Hello Volkan,
This is a bug when these options are used together, and will be fixed in the next patch.
Kind regards
Matthew
> Hello Everyone,
> I have a quick question. I am using FSL 5.0.4.
>
> I am using "mcflirt" with "-meanvol (register time-series to mean volume)" option to register my time-series images in a contrast enhancement study and it seems that using mean volume gives better registered images. Also, I am using "-mats" option to save transformation matrices (I need them because I have prior drown VOI's).
> When I checked the first one's transformation matrix (MAT0000), it is an 4x4 identity matrix (same with different data), which is unusual. Because when I compared the first time's registered and unregistered images, they are different.
>
> Also I am aware that "-meanvol" with "-plot" option had some issues
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0912&L=FSL&P=R34624&1=FSL&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4
>
> Is it a bug or I am missing something? Like all transformation matrixes are referenced to first transformed image? but then how can I find initial transformation matrix in the first place?
>
> Thanks in advance
> Volkan
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