Hello everybody
I write to you here because I have an issue with first_utils in the context of run_first_all.
Once I launch first_utils for a usual 2-group comparison, I receive the message:
"Abandon (core dumped)" after 3-4 minutes
The command line was:
first_utils --vertexAnalysis --usebvars -i L_Hipp_all.bvars -d design_con1_dis2.mat -o shape_analysis/L_Hipp_all --useReconNative --useRigidAlign -v >& shape_analysis/L_Hipp_all_output.txt
I did create the shape_analysis folder before launching the analysis.
When I take a look at the L_Hipp_all_output.txt created in the shape_analysis folder, it has the "recon and regnew design matrix", the following matrix, and then a message that says: "Image exception : #99:: Out of memory terminate called after throwing an instance of 'RBD_COMMON: Base Exception"
It goes like this:
read model
done reading model
setting up shape/appearance model
The shape has 732 vertices.
336 modes of variation are retained.
The model was constructed from 336 training subjects.
model loaded
read model
done reading model
setting up shape/appearance model
The shape has 732 vertices.
336 modes of variation are retained.
The model was constructed from 336 training subjects.
1.04257 0.018109 0.0551944 -12.7456
-0.0404429 1.04568 0.106556 -18.3057
-0.0556328 -0.112042 1.18776 -81.4009
0 0 0 1
0.994843 0.0116533 0.00758508 9.32513
0.0178276 1.0525 0.168465 -22.3169
-0.0128308 -0.26471 1.11538 -66.1825
0 0 0 1
1.0143 0.0773567 -0.0264502 -3.11034
-0.0527809 1.06914 0.137327 -21.8417
0.00369282 -0.194417 1.13972 -80.0795
0 0 0 1
1.02542 0.0469138 0.0332344 -9.66836
-0.05447 1.00414 0.314153 -32.5423
-0.0252935 -0.312117 1.05554 -47.2958
0 0 0 1
1.11874 -0.0464443 -0.0151247 -0.11898
0.0932306 1.03166 0.152162 -31.0216
0.0543581 -0.103916 1.1314 -92.7231
0 0 0 1
1.07847 -0.00632546 0.0273048 6.34585
-0.01568 1.11858 0.152583 -26.6022
-0.0079662 -0.200939 1.17707 -74.5386
0 0 0 1
1.05335 0.0592611 -0.0106399 -6.7955
-0.0574004 1.05263 0.2251 -37.242
0.031148 -0.227314 1.20805 -96.1348
0 0 0 1
0.999706 -0.0185871 0.0190071 16.453
0.0295471 1.08736 -0.025383 -4.67798
-0.011558 0.0259256 1.13515 -94.9377
0 0 0 1
1.00679 -0.0398368 0.0141123 11.5622
0.0392619 1.05469 0.161485 -27.79
-0.00629878 -0.248747 1.14329 -55.0713
0 0 0 1
0.959756 0.0701597 0.0780247 -7.44216
-0.0362812 1.13007 0.190609 -32.5457
-0.0780415 -0.246853 1.19299 -74.2754
0 0 0 1
0.94337 -0.0130446 -0.0295735 27.4177
0.0366757 0.994788 0.155896 -16.9482
0.0246369 -0.198841 1.10446 -73.5089
0 0 0 1
1.03336 0.0482007 -0.0542562 13.467
-0.0348148 1.09798 -0.00863795 -4.62244
0.0568462 -0.0141846 1.28138 -124.676
0 0 0 1
0.925676 -0.0222949 0.0247735 16.0736
0.0301071 1.04985 0.236886 -30.8738
-0.0306701 -0.262571 1.05107 -50.0185
0 0 0 1
1.01294 0.027297 0.0193414 6.09046
-0.0294611 0.999537 0.194832 -25.3939
-0.00430967 -0.260412 1.09845 -67.55
0 0 0 1
1.07514 0.0184993 -0.024445 4.85425
0.00792389 1.13942 0.00415302 -21.9924
0.0397035 0.0142257 1.30478 -132.079
0 0 0 1
1.01695 0.00370977 0.0172732 -1.41941
-0.00785718 1.01877 0.216672 -25.8125
0.00302726 -0.25171 1.19611 -77.2314
0 0 0 1
1.04146 0.0206388 0.02201 -7.95674
0.0297281 1.01167 0.122848 -12.5368
-0.0231665 -0.214371 1.12116 -66.9502
0 0 0 1
1.03918 0.018751 0.00591174 -4.34581
-0.00860384 1.03247 0.075199 -8.65141
-0.00911791 -0.150746 1.11174 -74.8946
0 0 0 1
1.1265 -0.0242775 0.0310541 -10.5395
0.0321152 0.993608 0.25286 -34.1399
-0.0200197 -0.268106 1.19959 -63.5708
0 0 0 1
1.02985 0.0388258 0.00931106 4.71022
-0.000820185 0.984618 0.129946 -8.25146
0.0077072 -0.186083 1.11649 -67.4352
0 0 0 1
1.00859 -0.00369912 0.00710884 6.39955
-0.0548144 1.0623 0.095865 -16.0579
0.0178416 -0.148721 1.13604 -78.4735
0 0 0 1
0.933988 -0.0216611 -0.00205944 10.6326
0.0369965 0.933852 0.375607 -39.7899
-0.00471514 -0.441287 1.05593 -26.1967
0 0 0 1
0.978001 0.0125283 -0.0404027 7.89304
-0.0177214 1.13949 0.0427299 -16.7415
0.0376763 -0.132698 1.13528 -85.2292
0 0 0 1
0.981985 0.0331239 -0.00133735 1.03648
-0.0122305 1.14615 0.0164112 -30.0827
-0.00724803 -0.0453953 1.22127 -99.3227
0 0 0 1
1.05422 0.0283989 0.01821 -10.5964
-0.0213531 1.12803 0.352564 -57.8714
-0.00518022 -0.403134 1.12161 -43.8488
0 0 0 1
1.14296 0.0374543 -0.00216867 -3.56351
-0.0434297 1.07258 0.0878189 -19.5977
-0.0148559 -0.0616307 1.21863 -115.208
0 0 0 1
1.03051 0.0226068 0.014093 13.7846
-0.0410837 1.07041 0.159543 -18.4681
-0.00795066 -0.188996 1.20242 -77.5334
0 0 0 1
1.01938 0.0179572 -0.0119456 14.1012
-0.118037 1.10214 0.179251 -14.2165
0.0187026 -0.213844 1.12863 -70.9903
0 0 0 1
1.02903 -0.0909255 -0.017443 18.0952
0.112266 1.08191 0.131796 -41.8843
0.00276433 -0.167924 1.21621 -86.3516
0 0 0 1
1.03357 0.0258616 0.0138856 12.475
-0.0248469 1.07844 0.188989 -18.5466
-0.00882558 -0.211172 1.13211 -71.8423
0 0 0 1
1.05084 0.0279959 -0.0197595 4.88539
0.00677272 1.02866 0.474452 -62.5627
0.0191962 -0.49903 1.19414 -53.8265
0 0 0 1
1.07492 -0.0167826 -0.0652372 4.7512
0.00904583 1.09083 0.176013 -34.0539
0.0278497 -0.257077 1.20605 -74.6272
0 0 0 1
1.06843 -0.00591492 -0.0391586 -1.05937
-0.0718972 1.04745 0.261706 -20.2766
0.0430981 -0.330166 1.1137 -62.417
0 0 0 1
1.0273 -0.0123238 -0.0322878 5.71735
0.0500262 1.12174 -0.0155666 -20.0765
0.0443028 -0.0118445 1.10997 -91.8702
0 0 0 1
1.04304 0.0291563 0.029371 7.05997
-0.0284673 1.14806 0.0778491 -29.7246
-0.0194182 -0.0874734 1.21051 -90.3479
0 0 0 1
1.04345 -0.0149341 0.050859 -6.38058
0.0192576 1.00341 0.325945 -40.3442
-0.0384334 -0.37338 1.14517 -42.782
0 0 0 1
1.10058 0.0411993 0.0191686 -5.94706
-0.0420016 1.09045 0.239128 -39.3045
-0.0140482 -0.262863 1.22908 -77.4559
0 0 0 1
1.07733 0.0281028 0.00996681 -2.14442
-0.0265968 1.11559 0.0703393 -23.8397
-0.0182156 -0.058911 1.28302 -105.195
0 0 0 1
1.15514 0.0174292 0.00672428 -14.9602
-0.0283924 1.02441 0.15149 -18.2741
-0.0293397 -0.20734 1.17223 -80.4058
0 0 0 1
0.945351 -0.0192571 -0.0179459 20.5339
0.0369033 1.05948 0.104612 -20.0682
0.0125839 -0.212769 1.12238 -74.886
0 0 0 1
0.984708 -0.0165877 0.0390234 15.104
-0.0155791 1.04932 0.433138 -53.2641
-0.0526709 -0.459681 1.12576 -12.4689
0 0 0 1
1.00578 -0.0326916 0.0306474 -0.214192
0.0241295 1.10834 0.249207 -47.6677
-0.0365241 -0.332224 1.21182 -65.8777
0 0 0 1
0.98266 0.0221138 0.05302 -4.81641
-0.0170428 0.943143 0.584914 -62.0744
-0.0407173 -0.561246 1.04134 -2.58595
0 0 0 1
1.01899 0.0346632 -0.0146447 -3.12401
-0.0355073 1.1025 0.0960117 -17.1168
0.0237455 -0.136844 1.14782 -73.7191
0 0 0 1
0.963867 0.0460552 0.0177328 -1.29234
-0.0540802 1.0617 0.184039 -32.8739
-0.00311442 -0.263872 1.17644 -59.545
0 0 0 1
1.01508 0.0319241 -0.0324287 4.4536
-0.0109734 1.10572 0.170704 -23.7069
0.0296509 -0.202018 1.16642 -80.5086
0 0 0 1
0.980851 0.0155475 0.0433229 -2.94324
0.00274705 1.03515 0.312936 -35.0826
-0.0272955 -0.355455 1.10209 -38.7166
0 0 0 1
1.00213 0.0153585 -0.00600255 0.886611
0.0177157 1.10472 0.177882 -27.8231
0.0177411 -0.226036 1.07978 -57.2572
0 0 0 1
1.05538 0.0424603 -0.015084 -4.53391
-0.0331327 1.07369 0.199881 -24.7325
0.0375859 -0.26667 1.20663 -71.3969
0 0 0 1
1.02835 0.0102341 -0.0322777 0.896698
-0.00495355 1.06486 0.406444 -49.7635
0.0254652 -0.386949 1.25865 -65.4127
0 0 0 1
1.09695 0.0225599 -0.0272073 -2.81019
0.00905738 1.07471 0.219976 -29.9016
0.0391135 -0.239309 1.10831 -64.5245
0 0 0 1
1.02934 0.0109241 -0.0312119 1.94804
-0.00385838 1.20301 0.0443615 -21.3162
0.00704407 -0.0599377 1.14681 -95.8592
0 0 0 1
1.00924 -0.0243636 0.0356413 -1.82094
0.0134236 0.996962 0.310748 -39.7405
-0.0444339 -0.261773 1.07619 -50.4821
0 0 0 1
1.0232 -0.0346888 -0.0208847 6.31734
0.0394611 1.01849 0.216473 -29.6231
5.15049e-05 -0.238126 1.19859 -82.3371
0 0 0 1
1.05418 0.0429542 -0.0207965 -4.17133
-0.034864 1.0758 0.252566 -46.0541
0.0305109 -0.27348 1.21706 -82.2206
0 0 0 1
1.1927 -0.0252578 0.0810563 -19.8883
-0.00266738 1.1103 0.145509 -25.0462
-0.0938482 -0.159373 1.19751 -78.0467
0 0 0 1
1.03749 0.0303056 -0.00601039 -4.54617
-0.00615396 1.08466 0.0949883 -16.5001
0.0094272 -0.152517 1.17745 -77.5725
0 0 0 1
1.02294 0.0571594 -0.00171094 4.33875
-0.0566763 1.16755 0.118416 -29.9266
0.00582415 -0.22616 1.16267 -77.8956
0 0 0 1
1.05829 -0.0308982 -0.0362609 10.1976
0.0514726 1.11679 0.0320384 -26.6924
0.0693389 -0.0134072 1.22988 -106.746
0 0 0 1
1.01509 0.045991 -0.0103087 -2.69453
-0.0474779 0.976889 0.102846 -0.621933
0.0226843 -0.133014 1.04579 -59.6241
0 0 0 1
1.03492 -0.0124728 -0.0594753 14.2498
0.0177463 1.07273 0.0919805 -15.4525
0.0637375 -0.122661 1.11705 -100.484
0 0 0 1
0.966465 0.0177576 -0.0388788 15.4437
0.0217668 0.909145 0.560658 -53.2968
0.0478761 -0.536518 1.04692 -16.9596
0 0 0 1
1.05494 -0.0830887 -0.0240928 13.8975
0.103791 0.955777 0.3779 -48.2582
-0.00116061 -0.37447 1.03103 -37.6164
0 0 0 1
1.05423 0.0251699 -0.044189 1.76738
-0.0246689 1.10642 0.232019 -32.8706
0.042187 -0.281869 1.13668 -62.1971
0 0 0 1
1.12521 0.0813901 0.0419089 -13.994
-0.0538234 1.08886 0.134687 -19.6119
-0.0328336 -0.174008 1.26778 -105.63
0 0 0 1
0.991703 0.0101242 -0.0102766 1.03295
-0.0367114 1.00449 0.129846 -13.7701
0.0399448 -0.117308 1.15731 -94.8628
0 0 0 1
1.00355 0.010075 -0.000567218 8.06997
-0.0304982 1.12438 0.21462 -41.4351
0.0118331 -0.175654 1.18166 -82.5168
0 0 0 1
1.06117 -0.0194646 -0.000402156 -1.8258
0.0103757 1.00894 0.319952 -38.424
-0.0156237 -0.30813 1.10184 -42.5482
0 0 0 1
1.05794 -0.0169495 -0.0276435 11.1047
0.00619726 1.09437 0.0388043 -19.4119
0.0173302 -0.0719681 1.18955 -82.313
0 0 0 1
1.09646 0.0543284 0.00369571 -1.55895
-0.0464429 1.00433 -0.0265725 4.454
0.00198095 -0.00147926 1.10058 -104.381
0 0 0 1
0.914579 0.0219204 0.00606818 14.8014
0.0197656 0.975573 0.250142 -28.0463
0.00333885 -0.301512 1.17301 -82.3438
0 0 0 1
1.0727 0.0618867 0.0954193 -15.8469
-0.0785671 0.975098 0.184064 -20.3343
-0.0768476 -0.201838 1.12355 -65.9581
0 0 0 1
0.999702 0.0635766 0.0438466 -9.83379
-0.0805273 1.01392 0.427214 -42.3835
-0.030614 -0.464955 1.09241 -19.371
0 0 0 1
0.953341 0.0597131 -0.0279489 2.85895
-0.0739135 1.13826 0.200771 -33.291
0.0183899 -0.14604 1.18765 -84.5313
0 0 0 1
1.01313 -0.0162094 -0.0172761 4.03109
0.0118665 1.03074 0.200178 -26.5096
0.00388649 -0.2372 1.18179 -66.5583
0 0 0 1
0.97202 0.0357855 0.0195076 0.867735
-0.00553868 0.972542 0.265389 -20.8058
-0.010669 -0.338777 1.09849 -33.2045
0 0 0 1
1.09591 -0.0272429 0.0976842 -13.285
0.0122265 1.1623 -0.0237185 -18.2145
-0.114775 -0.0283813 1.23898 -116.221
0 0 0 1
1.05634 -0.0142989 -0.0609126 12.9783
0.00789632 1.04857 0.161711 -36.5185
0.0649618 -0.131882 1.20027 -102.261
0 0 0 1
1.05621 0.0726672 -0.0124162 -2.38129
-0.0759923 1.03892 0.313868 -30.8214
0.0180176 -0.320419 1.1656 -63.636
0 0 0 1
1.09774 -0.016571 0.0585221 -14.6903
-0.0209325 1.10315 0.0821024 -25.0135
-0.0480604 -0.174839 1.10855 -53.247
0 0 0 1
1.01645 0.0742719 -0.0136162 -4.52898
-0.0442214 1.02925 0.184302 -16.8007
0.0415299 -0.233608 1.14181 -65.461
0 0 0 1
0.972036 -0.0875131 -0.0286407 25.162
0.0334569 1.03276 0.252315 -44.2801
0.0100386 -0.284816 1.16674 -73.2578
0 0 0 1
done recon
done recon and reg
new design matrix
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 -1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 1
Image Exception : #99 :: Out of memory
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
I'm running the analysis on Ubuntu 14.04 LTS, memory 1.8 Go, processer Intel Core 2 Duo CPU E8500 3.16 Ghz x2, OS type 32 bits
Could it be that the computer does not have enough memory to run such analyses? Or there may be a problem with the files I'm using?
Thank you very much
Shady
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