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.ht...
the "rms radial error" and "distance error " are below or see my attached log file.
$ 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
those are all fine - they are just measures of various energy functionals.
cheers Bruce On Wed, 19 Mar 2014, chenchunhuichina wrote:
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.h tml the "rms radial error" and "distance error " are below or see my attached log file. $ 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
chenchunhuichina