Hi Shady,
Yes, it looks like you need to run it on a machine with more memory (the output file it is trying to create is quite big). You may also need it to run it on a 64-bit platform as on a 32-bit one the amount of memory usable by the program is probably limited to 2GB.
Best,
Eelke
> On 29 Mar 2015, at 22:23, Shady Rahayel <[log in to unmask]> wrote:
>
> 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
|