Most of the information in an employee’s MySite profile comes from the Active Directory profile import, which is set up in the SharePoint Shared Service Provider.  However, this can be tricky with employee photos since links to photos are not normally stored in Active Directory.  An easy way around this if you don’t want to store the links in Active Directory, is to simply create a picture library in SharePoint and upload all of the employee photos to the picture library with a standard name, such as username.jpg.  Then you can write a script to update each MySite profile and associate the photo with the person.
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