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Sorry to keep adding information but I think is better that than waiting for you response and modifying everything then. I think I know how to compute the ROI mask but still I don’t know if that works. Because it is obtained from an atlas and the images I provide to fsl are not normalised or registered or anything. So they might not overlap properly in the region desired. May be once SIENA does its many steps it applies the mask and all goes well. But just wanted to verify. > On 5 Aug 2022, at 15:22, Andrade Rey René <[log in to unmask]> wrote: > > I have seen I can provide a mask for the ventricles. But my next question would be how to create this mask? Do I need to do it by hand or is there any automated pathway to do it? > >> On 5 Aug 2022, at 15:16, Andrade Rey René <[log in to unmask]> wrote: >> >> Dear community: >> >> I am getting in touch with you to see if there is any way to modify the parameters you pass into SIENA to modify the results of segmentation of VIENA. The 4th ventricle is pretty well but the 3rd not so much. >> >> Best, >> Rene Andrade. > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1 This message was issued to members of www.jiscmail.ac.uk/FSL, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/