What is happening is that FreeSurfer can (and often) change the volume dimensions, voxel size and of the input volume. So, after running FreeSurfer you still need to import to folder with the results. This will replace the original MRI with the T1.mgz MRI in the mri folder within the FreeSurfer results. This T1.mgz has the same volume size as the imported atlases.
As indicated in the tutorial:
[Section: Run FreeSurfer from Brainstorm] At the end, you need to call manually the menu Import anatomy folder described below.
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Import_the_results_in_Brainstorm