I am running 1000 possum simulations on a cluster and many of them crash with the error below. So far, none have generated a signal file. As you can (probably) determine from below, I am using a possum folder that has already been "possumed". That is, I have already run possum from this folder and generated a signal file. Now I am trying to switch the timecourse file each time to run 1000 simulations with noise added to the timecourse, rather than just thermal noise. Each time course file is cleverly named something like timecourse1, timecourse2, etc... and the output should be named signal1, signal2, etc...
Any help would be appreciated.
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The error file looks like this:
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
/opt/gridengine/default/spool/compute-30-4/job_scripts/385621: line 10: 30265 Aborted (core dumped) possum -i BasePossum/brain.nii.gz -x BasePossum/MRpar -m BasePossum/motion -p BasePossum/pulse -o BasePossum/Signal$SGE_TASK_ID -f BasePossum/slcprof -a BasePossum/T2.nii.gz -t timecourses/timecourse$SGE_TASK_ID.txt --nproc=1
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The output file looks like this:
Starting POSSUM...
Setting up the coordinate system...
Setting up the process ID...
Number of processors is 1.; My ID is 0.
Reading the object for ID 0...
object:: Size = (181,217,181,3)
object:: ROI Size = (181,217,181,3)
object:: Dims = (1,1,1,1)
object:: Minimum and maximum intensities are: 0 and 1
Reading the tissue properties...
T1,T2,SD,CS:
1.331000 0.051000 0.860000 0.000000
0.832000 0.044000 0.770000 0.000000
3.700000 0.500000 1.000000 0.000000
Reading the pulse sequence...
[SeqType,TE,TR,TRslc,Nx,Ny,dx,dy,maxG,RiseT,BW,Nvol,Nslc,SlcThk,SlcDir,Gap,zstart,FA]
1.000000 0.030000 3.000000 0.075000 64.000000 64.000000 0.003000 0.003000 0.035000 0.000200 143360.000000 140.000000 40.000000 0.003000 1.000000 0.000000 0.030000 90.000000 2.000000 3.000000 100.000000 1.000000
Reading the motion file...
Motion file is 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
Creating table for the slice profile...
Stepsize for the table: dslcp= 0.0154915
Calculating zstart, zend and level...
Slice selection direction is 1. (-+1 is z, -+2 is y and -+3 is x.)
Level is 1
Extra slc calculation...
Begining of the object is 28 and the end is 152 (in vox, in slice select direction).
Motion add on - side (mm):0; Motion add on + side (mm):0; Slice profile add:0.0022412
Extra voxels on - side:2& Extra voxels on + side (mm):2
Extra slices on - side:1 & Extra slices on + side:1
Creating activation4D volume and timecourse vector...
3D activation mode
Testing if the values in the activation volumes are smaller than the T2* values
vol= 0
vol= 1
vol= 2
vol= 3
vol= 4
vol= 5
vol= 6
vol= 7
vol= 8
vol= 9
vol= 10
vol= 11
vol= 12
vol= 13
vol= 14
vol= 15
vol= 16
vol= 17
vol= 18
vol= 19
vol= 20
vol= 21
vol= 22
vol= 23
vol= 24
vol= 25
vol= 26
vol= 27
vol= 28
vol= 29
vol= 30
vol= 31
vol= 32
vol= 33
vol= 34
vol= 35
vol= 36
vol= 37
vol= 38
vol= 39
vol= 40
vol= 41
vol= 42
vol= 43
vol= 44
vol= 45
vol= 46
vol= 47
vol= 48
vol= 49
vol= 50
vol= 51
vol= 52
vol= 53
vol= 54
vol= 55
vol= 56
vol= 57
vol= 58
vol= 59
vol= 60
vol= 61
vol= 62
vol= 63
vol= 64
vol= 65
vol= 66
vol= 67
vol= 68
vol= 69
vol= 70
vol= 71
vol= 72
vol= 73
vol= 74
vol= 75
vol= 76
vol= 77
vol= 78
vol= 79
vol= 80
vol= 81
vol= 82
vol= 83
vol= 84
vol= 85
vol= 86
vol= 87
vol= 88
vol= 89
vol= 90
vol= 91
vol= 92
vol= 93
vol= 94
vol= 95
vol= 96
vol= 97
vol= 98
vol= 99
vol= 100
vol= 101
vol= 102
vol= 103
vol= 104
vol= 105
vol= 106
vol= 107
vol= 108
vol= 109
vol= 110
vol= 111
vol= 112
vol= 113
vol= 114
vol= 115
vol= 116
vol= 117
vol= 118
vol= 119
vol= 120
vol= 121
vol= 122
vol= 123
vol= 124
vol= 125
vol= 126
vol= 127
vol= 128
vol= 129
vol= 130
vol= 131
vol= 132
vol= 133
vol= 134
vol= 135
vol= 136
vol= 137
vol= 138
vol= 139
Reading the RF inhomogeneity volumes...
RFobject:: Size = (181,217,181)
RFobject:: ROI Size = (181,217,181)
RFobject:: Dims = (1,1,1)
RFobject:: Minimum and maximum intensities are: 1 and 1
Calculating the signal...
Number of read out points is 22937600
LEVEL1
Creating 1 B0file together with 3 gradient files...
b0:: Size = (181,217,181)
b0:: ROI Size = (181,217,181)
b0:: Dims = (1,1,1)
b0:: Minimum and maximum intensities are: 0 and 0
Main loop...
Tissue type=0; zstart=28; zz=28; zend=153; Voxelnumber=0
Table sinc calc
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