A collimator located in a magnetic bunch compressor of a linear accelerator driven x-ray free electron laser has many potential applications, such as the removal of horns in the current distribution, the generation of ultra-short beams, and as a diagnostic of the beam slice emittance. Collective effects, however, are a major concern in applying the technique. Systematic measurements of emittance and analysis were performed using a collimator in the first bunch compressor of the Linac Coherent Light Source (LCLS). In the nominal, under-compressed configuration using the collimator we find that the y emittance (non-bending plane) is not increased, and the x emittance (in the bending plane) is increased by about 25%, in comparison to the injector emittance. From the analysis we conclude that the parasitic effects associated with this method are dominated by coherent synchrotron radiation (CSR), which causes a "systematic error" for measuring slice emittance at the bending plane using the collimation method. In general, we find good agreement between the measurements and simulations including CSR. However, for over-compressed beams at smaller collimator gaps, an extra emittance increase is found that does not agree with 1-D simulations and is not understood. Show Partial Abstract