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Hello,
I'm extracting some stats from recon-all but noticed that it would stop running in the middle (error message: end: Not in while/foreach) . Any suggestions on how I could solve this problem would be greatly appreciated! Thank you so much in advance.
Best regards, Da-Yea
computing statistics for each annotation in rantaFL.annot. reading volume /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/mri/wm.mgz... reading input surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/lh.white... Using TH3 vertex volume calc Total face volume 249500 Total vertex volume 245871 (mask=0) reading input pial surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/lh.pial... reading input white surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/lh.white... reading colortable from annotation file... colortable with 11 entries read (originally /freesurfer/FrontalLobeColorLUT.txt) atlas_icv (eTIV) = 1377325 mm^3 (det: 1.414413 ) lhCtxGM: 245607.578 244866.000 diff= 741.6 pctdiff= 0.302 rhCtxGM: 253269.330 252721.000 diff= 548.3 pctdiff= 0.217 lhCtxWM: 199421.968 199714.500 diff= -292.5 pctdiff=-0.147 rhCtxWM: 198426.788 199552.500 diff=-1125.7 pctdiff=-0.567 SubCortGMVol 53103.000 SupraTentVol 962619.664 (961451.000) diff=1168.664 pctdiff=0.121 SupraTentVolNotVent 951172.664 (950004.000) diff=1168.664 pctdiff=0.123 BrainSegVol 1091475.000 (1088903.000) diff=2572.000 pctdiff=0.236 BrainSegVolNotVent 1076628.000 (1076311.664) diff=316.336 pctdiff=0.029 BrainSegVolNotVent 1076628.000 CerebellumVol 126436.000 VentChorVol 11447.000 3rd4th5thCSF 3400.000 CSFVol 828.000, OptChiasmVol 188.000 MaskVol 1502516.000 structure is "anterior_cingulate" number of vertices = 3531 total surface area = 2414 mm^2 total gray matter volume = 6657 mm^3 average cortical thickness = 2.742 mm +- 0.824 mm average integrated rectified mean curvature = 0.116 average integrated rectified Gaussian curvature = 0.017 folding index = 37 intrinsic curvature index = 2.5 structure is "dlpfc" number of vertices = 10762 total surface area = 7059 mm^2 total gray matter volume = 20651 mm^3 average cortical thickness = 2.426 mm +- 0.665 mm average integrated rectified mean curvature = 0.125 average integrated rectified Gaussian curvature = 0.025 folding index = 150 intrinsic curvature index = 10.8 structure is "frontal_eye_field" number of vertices = 1371 total surface area = 927 mm^2 total gray matter volume = 2587 mm^3 average cortical thickness = 2.654 mm +- 0.526 mm average integrated rectified mean curvature = 0.111 average integrated rectified Gaussian curvature = 0.020 folding index = 12 intrinsic curvature index = 1.0 structure is "inferolateral_pfc" number of vertices = 4430 total surface area = 2928 mm^2 total gray matter volume = 9914 mm^3 average cortical thickness = 2.662 mm +- 0.654 mm average integrated rectified mean curvature = 0.124 average integrated rectified Gaussian curvature = 0.022 folding index = 64 intrinsic curvature index = 4.1 structure is "lateral_OFC" number of vertices = 5859 total surface area = 3926 mm^2 total gray matter volume = 11128 mm^3 average cortical thickness = 2.493 mm +- 0.732 mm average integrated rectified mean curvature = 0.128 average integrated rectified Gaussian curvature = 0.029 folding index = 74 intrinsic curvature index = 6.6 structure is "medial_OFC" number of vertices = 1871 total surface area = 1217 mm^2 total gray matter volume = 3722 mm^3 average cortical thickness = 2.641 mm +- 0.791 mm average integrated rectified mean curvature = 0.121 average integrated rectified Gaussian curvature = 0.036 folding index = 27 intrinsic curvature index = 2.9 structure is "mpfc" number of vertices = 6801 total surface area = 4531 mm^2 total gray matter volume = 15597 mm^3 average cortical thickness = 2.761 mm +- 0.652 mm average integrated rectified mean curvature = 0.127 average integrated rectified Gaussian curvature = 0.027 folding index = 86 intrinsic curvature index = 7.4 structure is "primary_motor" number of vertices = 6578 total surface area = 3910 mm^2 total gray matter volume = 12307 mm^3 average cortical thickness = 2.729 mm +- 0.549 mm average integrated rectified mean curvature = 0.094 average integrated rectified Gaussian curvature = 0.016 folding index = 52 intrinsic curvature index = 4.3 structure is "supplementary_motor_complex" number of vertices = 2427 total surface area = 1664 mm^2 total gray matter volume = 5088 mm^3 average cortical thickness = 2.595 mm +- 0.593 mm average integrated rectified mean curvature = 0.121 average integrated rectified Gaussian curvature = 0.023 folding index = 25 intrinsic curvature index = 2.2 structure is "lateral_premotor" number of vertices = 3941 total surface area = 2586 mm^2 total gray matter volume = 7468 mm^3 average cortical thickness = 2.642 mm +- 0.522 mm average integrated rectified mean curvature = 0.105 average integrated rectified Gaussian curvature = 0.023 folding index = 35 intrinsic curvature index = 4.1 computing statistics for each annotation in rantaFL.annot. reading volume /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/mri/wm.mgz... reading input surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/rh.white... Using TH3 vertex volume calc Total face volume 257391 Total vertex volume 253779 (mask=0) reading input pial surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/rh.pial... reading input white surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/rh.white... reading colortable from annotation file... colortable with 11 entries read (originally /freesurfer/FrontalLobeColorLUT.txt) atlas_icv (eTIV) = 1377325 mm^3 (det: 1.414413 ) lhCtxGM: 245607.578 244866.000 diff= 741.6 pctdiff= 0.302 rhCtxGM: 253269.330 252721.000 diff= 548.3 pctdiff= 0.217 lhCtxWM: 199421.968 199714.500 diff= -292.5 pctdiff=-0.147 rhCtxWM: 198426.788 199552.500 diff=-1125.7 pctdiff=-0.567 SubCortGMVol 53103.000 SupraTentVol 962619.664 (961451.000) diff=1168.664 pctdiff=0.121 SupraTentVolNotVent 951172.664 (950004.000) diff=1168.664 pctdiff=0.123 BrainSegVol 1091475.000 (1088903.000) diff=2572.000 pctdiff=0.236 BrainSegVolNotVent 1076628.000 (1076311.664) diff=316.336 pctdiff=0.029 BrainSegVolNotVent 1076628.000 CerebellumVol 126436.000 VentChorVol 11447.000 3rd4th5thCSF 3400.000 CSFVol 828.000, OptChiasmVol 188.000 MaskVol 1502516.000 structure is "anterior_cingulate" number of vertices = 3332 total surface area = 2321 mm^2 total gray matter volume = 6663 mm^3 average cortical thickness = 2.866 mm +- 0.804 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.020 folding index = 46 intrinsic curvature index = 2.4 structure is "dlpfc" number of vertices = 9975 total surface area = 6648 mm^2 total gray matter volume = 19598 mm^3 average cortical thickness = 2.528 mm +- 0.591 mm average integrated rectified mean curvature = 0.122 average integrated rectified Gaussian curvature = 0.024 folding index = 131 intrinsic curvature index = 9.7 structure is "frontal_eye_field" number of vertices = 1041 total surface area = 716 mm^2 total gray matter volume = 2230 mm^3 average cortical thickness = 2.746 mm +- 0.497 mm average integrated rectified mean curvature = 0.113 average integrated rectified Gaussian curvature = 0.019 folding index = 9 intrinsic curvature index = 0.8 structure is "inferolateral_pfc" number of vertices = 5727 total surface area = 3741 mm^2 total gray matter volume = 13361 mm^3 average cortical thickness = 2.918 mm +- 0.711 mm average integrated rectified mean curvature = 0.129 average integrated rectified Gaussian curvature = 0.027 folding index = 81 intrinsic curvature index = 6.0 structure is "lateral_OFC" number of vertices = 5282 total surface area = 3577 mm^2 total gray matter volume = 10853 mm^3 average cortical thickness = 2.722 mm +- 0.712 mm average integrated rectified mean curvature = 0.128 average integrated rectified Gaussian curvature = 0.031 folding index = 68 intrinsic curvature index = 6.3 structure is "medial_OFC" number of vertices = 2515 total surface area = 1658 mm^2 total gray matter volume = 4981 mm^3 average cortical thickness = 2.630 mm +- 0.880 mm average integrated rectified mean curvature = 0.137 average integrated rectified Gaussian curvature = 0.043 folding index = 41 intrinsic curvature index = 4.8 structure is "mpfc" number of vertices = 7124 total surface area = 4660 mm^2 total gray matter volume = 17198 mm^3 average cortical thickness = 3.001 mm +- 0.598 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.030 folding index = 90 intrinsic curvature index = 8.8 structure is "primary_motor" number of vertices = 7001 total surface area = 4241 mm^2 total gray matter volume = 13708 mm^3 average cortical thickness = 2.789 mm +- 0.539 mm average integrated rectified mean curvature = 0.101 average integrated rectified Gaussian curvature = 0.016 folding index = 56 intrinsic curvature index = 4.7 structure is "supplementary_motor_complex" number of vertices = 2086 total surface area = 1420 mm^2 total gray matter volume = 4986 mm^3 average cortical thickness = 3.022 mm +- 0.623 mm average integrated rectified mean curvature = 0.108 average integrated rectified Gaussian curvature = 0.018 folding index = 19 intrinsic curvature index = 1.5 structure is "lateral_premotor" number of vertices = 3371 total surface area = 2278 mm^2 total gray matter volume = 7004 mm^3 average cortical thickness = 2.809 mm +- 0.586 mm average integrated rectified mean curvature = 0.101 average integrated rectified Gaussian curvature = 0.017 folding index = 29 intrinsic curvature index = 2.3 end: Not in while/foreach.
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