Hi there,
I have trying to run VIENA with an user supplied mask.
I noticed that VIENA looks in the folder made by SIENA, which is a bit odd as this folder will not exist before running SIENA with the -V and -v mask option. Solution is to run it again with the mask copied to the siena folder, or use a relative path: -v ../mask
Also, in viena script it attempts to transform the usersupplied mask with the avgMNI template transformmatrix (flirt-applyxfm) , while the user supplied mask is already in native space, thus leading to an error. I am now modifying the viena script so it skips the applyxfm.
Did anyone else experienced this?
Best,
Jeroen
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