The patch operation is needed to get spatial derivatives and prepare CIV2. It provides an interpolation on a regular grid (interp) and an interpolation with smoothing ( filter). Both fields are stored in the same netcdf file as the CIV1 results.
Run the patch programme by the web interface at address http://Z4/CIV/interpolation.htm. Select the .civ file and click processing options, which yields a new web page. Introduce the image organisation options like for CIV1 and the number of grid points on which interpolation has to be done in each direction: the programme puts grid points at the minimum and maximum x coordinates of the initial civ grid and divides the length in regular intervals. Choose by default the same number of grid points as in CIV1. Select the same image pair as for CIV1.
Then set the spline parameters. Because of computation cost, the spline
is restricted to sub-domains (with smooth matching). The default number
400 of points for a sub-domain is a good compromise. The smoothing
increases for increasing parameters 
. Use the default
value 1 as a first guess.
The result of patch can be checked by uvmat, selecting the fields interp or filter. You can see the difference between these two fields, and get the corresponding histogram, by selecting both options simultaneously. For an optimum smoothing, the difference between filter and interp should be of the order of the measurement error, typically 0.2 pixel. You can even use higher values, as this smoothing is later used only to estimate the deformation of the fluid elements, while the velocity vectors are determined again from the images at each civ iteration.
By looking at the difference between civ1 and filter,
you can further eliminate false vectors. Run fix_vel,
selecting both civ_1 and filter, to remove
vectors such that this difference is beyond a threshold. Choose a
threshold value about 1 pixel, depending on the field quality. The
vectors removed by this criterium have a FixFlag with 1 as the second
digit (e.g. FixFlag=100 in the absence of other rejection criteria).
You can then run again the patch programme with this improved field,
and possibly with a better adjusted .