Dear Arnaud,
Maybe you can provide the exact error message from Matlab window plus look into the analysis folder = which files are generated before the estimation stops? How do the functional images forwarded into the analysis look like? "There are no significant voxels." has been reported rather frequently, usually for group models, but it's related to the non-sphericity correction and not the voxel size.
> At the end of the preprocessing I have anat and bold images of 1mm3
Which resolution did you use during fMRI data acquisition? If it's an average resolution, e.g. 3x3x3 mm^3, it should be sufficient to apply the flow fields and resample to e.g. the usual 2x2x2 mm^3 for the BOLD series.
Best
Helmut
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