Arun,
The SCXI-1125 can be configured to have either a 4 Hz or a 10 kHz filter to eliminate noise in the signal. With this filter the noise you are experiencing should not affect your measurements.
You can read more about the SCXI-1125 and filters in the user manual:
http://digital.ni.com/manuals.nsf/websearch/85C7726245BE7391862567BE0056BAFD?OpenDocument&node=132100_US
-Sal