The mask has to be a 3-dimensional binary volume. I'm not sure there is a way to do what (I think) you want to do (would not make sense).

       

Dear freesurfer experts,

I would like to ask you about the mris_fwhm script. What does the flag "--mask" exactly do? Suppose I would like to compute the effective smoothness of an mri dataset. Some subjects have zeros in some vertices, but instead of using the prune option, I would like to use all the available signal, so I have to use a different mask for every subject. Would the option mask do the job in that case and would accept the multidimensional mask? Or rather the "--mask" option expects for a single (not multidimensional) mask?

Any insight would be greatly appreciated. Thanks in advance,
Eduard Vilaplana.

Unitat de Memòria/Memory Unit
Servei de Neurologia/Neurology Department
Hospital de la Santa Creu i Sant Pau
Sant Antoni Mª Claret 167
Barcelona 08025
Spain
(Tel) +34 93 556 59 86 (ext 8229)
Email:evilaplana@santpau.cat
http://santpaumemoryunit.com/

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