Comparison of FreeSurfer and CAT12 Software in Parcel-Based Cortical Thickness Calculations.

Several approaches have emerged to measure the cortical thickness (CT), which can be broadly divided into surface-based and voxel-based algorithms. We aimed to compare parcel-based CT estimation of the widely used FreeSurfer (FS) software and CAT12 software, which is a widely used voxel-based approach, and evaluate the test-retest (TRT) reliability of both methods. MRI images of 417 healthy individuals were analyzed. TRT reliability was performed on 60 participants. The mean CT of the parcels of the Desikan-Killiany atlas were calculated both in FS and CAT12. Linear mixed model was performed to compare the two methods and the TRT reliability, and paired-sample t-test for post-hoc analyses. Linear regression analyses were utilized to examine the regressions between the two methods and between different sessions with each method. CT values calculated using the two methods were significantly correlated (R 2 adj  = 0.67). The significant interaction effect between the method and the parcels were due to larger CT values of FS in 32 of 68 parcels, whereas CT values of CAT12 were higher in 31 of 68 parcels. The TRT reliabilities of both approaches were excellent (FS R 2 adj  = 0.95, CAT12 R 2 adj  = 0.93). We conclude that both techniques can provide equally valid results for groups comparisons or follow-up studies as long as they are not mixed with each other.