Dear Freesurfers,
I am new to freesurfer and I am afraid of doing something wrong, so I am
writing to ask is this error indicating something wrong with my data?
Any help is appreciated. below are detials of my question. Thank you!
I used
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
with this command
fsl_sub -N cch recon-all -i ${i} -s FSsub${i:3:5} -all
I checked the O file from fsl_sub and it said at the end
"recon-all -s FSsub12534 finished without error at Thu Jan 23 15:44:35 CST 2014
done"
Seems it's OK
then checked the e file from fsl_sub
(standard_in) 2: Error: comparison in expression
Seems this is a problem of fsl_sub, According to
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-May/023961.html
I guess I can ignore it?
Then I checked the recon-all.log file and find a lot of "error",
Someone asked this question and got the answer "We see this mysterious message
sometimes...usually things are fine". So when and why get there errors and does
they always fine?
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-October/020810.html
the "rms radial error" and "distance error " are below .
$ grep -n error FSsub12534/scripts/recon-all.log
2931:inflating to sphere (rms error < 2.00)
2932:000: dt: 0.0000, rms radial error=176.789, avgs=0
2933:005/300: dt: 0.9000, rms radial error=176.532, avgs=0
2934:010/300: dt: 0.9000, rms radial error=175.978, avgs=0
2935:015/300: dt: 0.9000, rms radial error=175.253, avgs=0
2936:020/300: dt: 0.9000, rms radial error=174.426, avgs=0
2937:025/300: dt: 0.9000, rms radial error=173.543, avgs=0
2938:030/300: dt: 0.9000, rms radial error=172.627, avgs=0
2939:035/300: dt: 0.9000, rms radial error=171.693, avgs=0
2940:040/300: dt: 0.9000, rms radial error=170.750, avgs=0
2941:045/300: dt: 0.9000, rms radial error=169.806, avgs=0
2942:050/300: dt: 0.9000, rms radial error=168.861, avgs=0
2943:055/300: dt: 0.9000, rms radial error=167.919, avgs=0
2944:060/300: dt: 0.9000, rms radial error=166.980, avgs=0
2945:065/300: dt: 0.9000, rms radial error=166.045, avgs=0
2946:070/300: dt: 0.9000, rms radial error=165.114, avgs=0
2947:075/300: dt: 0.9000, rms radial error=164.188, avgs=0
2948:080/300: dt: 0.9000, rms radial error=163.267, avgs=0
2949:085/300: dt: 0.9000, rms radial error=162.351, avgs=0
2950:090/300: dt: 0.9000, rms radial error=161.439, avgs=0
2951:095/300: dt: 0.9000, rms radial error=160.532, avgs=0
2952:100/300: dt: 0.9000, rms radial error=159.629, avgs=0
2953:105/300: dt: 0.9000, rms radial error=158.732, avgs=0
2954:110/300: dt: 0.9000, rms radial error=157.839, avgs=0
2955:115/300: dt: 0.9000, rms radial error=156.951, avgs=0
2956:120/300: dt: 0.9000, rms radial error=156.068, avgs=0
2957:125/300: dt: 0.9000, rms radial error=155.189, avgs=0
2958:130/300: dt: 0.9000, rms radial error=154.316, avgs=0
2959:135/300: dt: 0.9000, rms radial error=153.447, avgs=0
2960:140/300: dt: 0.9000, rms radial error=152.583, avgs=0
2961:145/300: dt: 0.9000, rms radial error=151.723, avgs=0
2962:150/300: dt: 0.9000, rms radial error=150.868, avgs=0
2963:155/300: dt: 0.9000, rms radial error=150.018, avgs=0
2964:160/300: dt: 0.9000, rms radial error=149.173, avgs=0
2965:165/300: dt: 0.9000, rms radial error=148.332, avgs=0
2966:170/300: dt: 0.9000, rms radial error=147.496, avgs=0
2967:175/300: dt: 0.9000, rms radial error=146.665, avgs=0
2968:180/300: dt: 0.9000, rms radial error=145.838, avgs=0
2969:185/300: dt: 0.9000, rms radial error=145.015, avgs=0
2970:190/300: dt: 0.9000, rms radial error=144.198, avgs=0
2971:195/300: dt: 0.9000, rms radial error=143.384, avgs=0
2972:200/300: dt: 0.9000, rms radial error=142.576, avgs=0
2973:205/300: dt: 0.9000, rms radial error=141.771, avgs=0
2974:210/300: dt: 0.9000, rms radial error=140.971, avgs=0
2975:215/300: dt: 0.9000, rms radial error=140.176, avgs=0
2976:220/300: dt: 0.9000, rms radial error=139.385, avgs=0
2977:225/300: dt: 0.9000, rms radial error=138.598, avgs=0
2978:230/300: dt: 0.9000, rms radial error=137.816, avgs=0
2979:235/300: dt: 0.9000, rms radial error=137.039, avgs=0
2980:240/300: dt: 0.9000, rms radial error=136.265, avgs=0
2981:245/300: dt: 0.9000, rms radial error=135.496, avgs=0
2982:250/300: dt: 0.9000, rms radial error=134.731, avgs=0
2983:255/300: dt: 0.9000, rms radial error=133.971, avgs=0
2984:260/300: dt: 0.9000, rms radial error=133.215, avgs=0
2985:265/300: dt: 0.9000, rms radial error=132.463, avgs=0
2986:270/300: dt: 0.9000, rms radial error=131.715, avgs=0
2987:275/300: dt: 0.9000, rms radial error=130.972, avgs=0
2988:280/300: dt: 0.9000, rms radial error=130.232, avgs=0
2989:285/300: dt: 0.9000, rms radial error=129.497, avgs=0
2990:290/300: dt: 0.9000, rms radial error=128.766, avgs=0
2991:295/300: dt: 0.9000, rms radial error=128.039, avgs=0
2992:300/300: dt: 0.9000, rms radial error=127.316, avgs=0
3017:distance error %100000.00
3572:pass 1: epoch 1 of 3 starting distance error %19.12
3573:pass 1: epoch 2 of 3 starting distance error %19.11
3575:starting distance error %19.02
3577:final distance error %19.05
4618:inflating to sphere (rms error < 2.00)
4619:000: dt: 0.0000, rms radial error=176.609, avgs=0
4620:005/300: dt: 0.9000, rms radial error=176.351, avgs=0
4621:010/300: dt: 0.9000, rms radial error=175.799, avgs=0
4622:015/300: dt: 0.9000, rms radial error=175.074, avgs=0
4623:020/300: dt: 0.9000, rms radial error=174.248, avgs=0
4624:025/300: dt: 0.9000, rms radial error=173.365, avgs=0
4625:030/300: dt: 0.9000, rms radial error=172.450, avgs=0
4626:035/300: dt: 0.9000, rms radial error=171.518, avgs=0
4627:040/300: dt: 0.9000, rms radial error=170.578, avgs=0
4628:045/300: dt: 0.9000, rms radial error=169.635, avgs=0
4629:050/300: dt: 0.9000, rms radial error=168.695, avgs=0
4630:055/300: dt: 0.9000, rms radial error=167.757, avgs=0
4631:060/300: dt: 0.9000, rms radial error=166.822, avgs=0
4632:065/300: dt: 0.9000, rms radial error=165.892, avgs=0
4633:070/300: dt: 0.9000, rms radial error=164.966, avgs=0
4634:075/300: dt: 0.9000, rms radial error=164.044, avgs=0
4635:080/300: dt: 0.9000, rms radial error=163.127, avgs=0
4636:085/300: dt: 0.9000, rms radial error=162.215, avgs=0
4637:090/300: dt: 0.9000, rms radial error=161.307, avgs=0
4638:095/300: dt: 0.9000, rms radial error=160.405, avgs=0
4639:100/300: dt: 0.9000, rms radial error=159.507, avgs=0
4640:105/300: dt: 0.9000, rms radial error=158.613, avgs=0
4641:110/300: dt: 0.9000, rms radial error=157.725, avgs=0
4642:115/300: dt: 0.9000, rms radial error=156.841, avgs=0
4643:120/300: dt: 0.9000, rms radial error=155.961, avgs=0
4644:125/300: dt: 0.9000, rms radial error=155.086, avgs=0
4645:130/300: dt: 0.9000, rms radial error=154.217, avgs=0
4646:135/300: dt: 0.9000, rms radial error=153.351, avgs=0
4647:140/300: dt: 0.9000, rms radial error=152.490, avgs=0
4648:145/300: dt: 0.9000, rms radial error=151.634, avgs=0
4649:150/300: dt: 0.9000, rms radial error=150.783, avgs=0
4650:155/300: dt: 0.9000, rms radial error=149.936, avgs=0
4651:160/300: dt: 0.9000, rms radial error=149.094, avgs=0
4652:165/300: dt: 0.9000, rms radial error=148.256, avgs=0
4653:170/300: dt: 0.9000, rms radial error=147.423, avgs=0
4654:175/300: dt: 0.9000, rms radial error=146.594, avgs=0
4655:180/300: dt: 0.9000, rms radial error=145.770, avgs=0
4656:185/300: dt: 0.9000, rms radial error=144.950, avgs=0
4657:190/300: dt: 0.9000, rms radial error=144.135, avgs=0
4658:195/300: dt: 0.9000, rms radial error=143.324, avgs=0
4659:200/300: dt: 0.9000, rms radial error=142.517, avgs=0
4660:205/300: dt: 0.9000, rms radial error=141.715, avgs=0
4661:210/300: dt: 0.9000, rms radial error=140.918, avgs=0
4662:215/300: dt: 0.9000, rms radial error=140.125, avgs=0
4663:220/300: dt: 0.9000, rms radial error=139.336, avgs=0
4664:225/300: dt: 0.9000, rms radial error=138.552, avgs=0
4665:230/300: dt: 0.9000, rms radial error=137.771, avgs=0
4666:235/300: dt: 0.9000, rms radial error=136.995, avgs=0
4667:240/300: dt: 0.9000, rms radial error=136.223, avgs=0
4668:245/300: dt: 0.9000, rms radial error=135.455, avgs=0
4669:250/300: dt: 0.9000, rms radial error=134.692, avgs=0
4670:255/300: dt: 0.9000, rms radial error=133.933, avgs=0
4671:260/300: dt: 0.9000, rms radial error=133.178, avgs=0
4672:265/300: dt: 0.9000, rms radial error=132.427, avgs=0
4673:270/300: dt: 0.9000, rms radial error=131.680, avgs=0
4674:275/300: dt: 0.9000, rms radial error=130.938, avgs=0
4675:280/300: dt: 0.9000, rms radial error=130.200, avgs=0
4676:285/300: dt: 0.9000, rms radial error=129.466, avgs=0
4677:290/300: dt: 0.9000, rms radial error=128.736, avgs=0
4678:295/300: dt: 0.9000, rms radial error=128.011, avgs=0
4679:300/300: dt: 0.9000, rms radial error=127.289, avgs=0
4704:distance error %100000.00
5218:pass 1: epoch 1 of 3 starting distance error %19.52
5219:pass 1: epoch 2 of 3 starting distance error %19.45
5221:starting distance error %19.40
5223:final distance error %19.42
9439:recon-all -s FSsub12534 finished without error at Thu Jan 23 15:44:35 CST
2014
2014-03-19
Chunhui Chen
_________________
State Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875
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