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.