these look like normal variations of the measures with repeated runs. Certainly 2% test/retest is nothing to worry about. I think that randomness is now off by default, but Nick can confirm.

cheers, Bruce

On Tue, 20 Oct 2009, leemon albert wrote:

Hi,

We run the freesurfer stable v4.4.0 on our Linux computer (Ubuntu 9.04). The program finishes without any error. However, we find the stats files (in the /subject/stats) from repeated runs on the same subject vary widely in final outcome. Meanwhile, we notice the item of the stable v4.5.0 release notes, which's about the flag of -norandomness. It's said that the binaries in the recon-all stream are subject to variability due to usage of a random number generator (mris_smooth, mris_sphere, mris_topology_fixer, mris_topo_fixer and mris_ca_label). Is this realtive with our problem? Have anyone met this problem? Do the data need to rerun using Stable v4.5.0? To take into account the number of the subjects, is there any other method to fix it?

For example: tail -2 'thickness.lh.MT.songjunyi.txt' # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd lh.MT.songjunyi.label 2330 1564 4584 2.548 0.684 0.146 0.062 52 6.5 tail -2 thickness.lh.MT.songjunyi_re1.txt # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd lh.MT.songjunyi_re1.label 2409 1631 4786 2.539 0.698 0.146 0.075 78 7.7 tail -2 thickness.lh.MT.songjunyi_re2.txt # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd lh.MT.songjunyi_re2.label 2341 1576 4659 2.558 0.694 0.143 0.058 39 6.0

Any help would be appreciated. Thanks.