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Branding in NBIA is accomplished by editing and or replacing the objects in the branding folders found in /software/common/resources/branding.  The nbia folder contained within is the default branding for NBIA.  The sub folder images contains the customizable images for the application, they include:

NameDimensions
FNLfCR-LOGO.png 200 x 39
footer_usagov.gif127 x 31
Logo-NCIA.jpg500 x  53
nci-header.png300 x 38
nci-link.png300 x 38
NCI-logo-white.png54 x 32
NCICBLOGO.gif126 x 43
white-ncilogo.gif263 x 39
white-nciurl.gif99 x 39
white-nihtext.gif208 x 39

To use your own images simply replace the image while keeping the same name as the original one in your new folder, and the build will update it accordingly.  At the base level of the folder are the XHTML/properties files that allow customization, the include:

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The Quick Links XHTML is imported into the scope of an XHTML table. Any XHTML specified here should be wrapped in a <tr> and at least one <td> element.
For an example see: https://ncisvn.nci.nih.gov/svn/nbia/trunk/docs/deployment/niams_brandinggithub.com/CBIIT/national-biomedical-image-archive/blob/master/software/common/resources/branding/niams/quickLinks.xhtml

Other XHTML

There are no restrictions on XHTML for the welcome title/text or the footer.