DR-BUDDI Memory Allocation Error (out of memory)

[Bryan Fishman]

Greetings,

DR-BUDDI is running out of RAM while running SyN registration.  The server running the program has 64 Gigabytes of RAM, and sure enough, all of it is steadily used until none is left and the program crashes.

Interestingly, other data sets (including larger ones) do not encounter the same issue.  Is this a possible bug in the latest version of DR-BUDDI?  Is there a way to reduce the RAM usage without sacrificing (much) quality?

Thank you for any assistance you may be able to provide!

[Pablo Velasco]

Hi All,

I got a similar error (maybe the same) in one of the intermediate steps of Dr-Buddi.

The command I ran was:

/CBI/bin/TORTOISE/DRBUDDIV31/bin/DR_BUDDI_withoutGUI --up_data dMRI_AP_1.0_proc/dMRI_AP_1.0_proc.list --down_data dMRI_PA_1.0_proc/dMRI_PA_1.0_proc.list --structural __t2_space_sag_p2_iso_20171026111953_5.nii --distortion_level large --n_DWIs 6 --final_signal_modulation Jac --restrict-deformation 1 --corr_window_size 80 --enforce_deformation_antisymmetry 1 --output ./test_DR_BUDDI

The error I get is:

Exception caught:
itk::MemoryAllocationError (0x7f28300437e0)
Location: "unknown"
File: /stbb_home/irfanogo/Desktop/codes/other_codes/ANTS_05_23_2014/antsbin/InsightToolkit-4.12.0/Modules/Core/Common/include/itkImportImageContainer.hxx
Line: 199
Description: Failed to allocate memory for image.

The program continues running until completion, but the images I get are not corrected at all.

Any ideas of what can be wrong?

This is the output I get (trimmed a little bit):

Transforming volume: 0

Transforming volume: 1

Transforming volume: 2

[...]

Transforming volume: 141

Transforming volume: 142

Computing Tensors...

Transforming volume: 0

Transforming volume: 1

Transforming volume: 2

[...]

Transforming volume: 141

Transforming volume: 142

Computing Tensors...

Rigidly registering the structural image to the b0_up image...

Iteration : 1   -0.339774,    [1.8221491980643787, 5.74025227268743, -2.46734498596478, -0.05542098060620889, 0.04657984410404975, -0.019591657201182323, 0.0459847811871907, 1.1146879122042122, -0.00013885007927519875, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]

[...]

Rigidly registering the b0_down to the structural image...

Iteration : 1   -0.197692,    [-0.06597725380104702, 0.6932453482581468, -0.12024537650095024, 0.013681290946743547, 0.0033400945441941898, 0.0019443861533532387, -0.002230769080747267, 1.0076123795229488, -0.01446985114940438, 0.00007346390566014852, 0.000047923967511116906, 0.00000807347641963206, -0.0004303220263861177, -0.0002576383350197984, 0, 0, 0, 0, 0, 0, 0]

[...]

  number of levels = 4

  iterations = 60x60x60x60

Current learning rate: 12.5

  convergence threshold = 5e-06

  convergence window size = 10

  number of levels = 4

  using the CCSK metric (radius = 80, weight = 1.5)

  using the MSJac metric (radius = , weight = 0.5)

  using the MSJac metric (radius = , weight = 0.5)

  using the MSJac metric (radius = , weight = 0.5)

  using the MSJac metric (radius = , weight = 0.5)

Number of time points: 7

*** Running time-varying velocity field registration (varianceForUpdateField = 5, varianceForTotalField = 0.5, varianceForUpdateFieldTime = 0.75, varianceForTotalFieldTime = 0.1) ***

  Current level = 1 of 4

    number of iterations = 60

    shrink factors = [6, 6, 6]

    smoothing sigmas = 0.6 vox

    required fixed parameters = [49, 45, 30, 7, -78.09438700342126, -79.44791582118359, -41.643936159621276, 0, 3.0000035762786865, 3, 3, 1, 0.9987591399204215, -0.017259023951264815, -0.04671516205346462, 0, 0.017233051097196844, 0.9998510403254234, -0.0009587218387751775, 0, 0.04672475120641155, 0.00015248743758484006, 0.9989077907828903, 0, 0, 0, 0, 1]

Iteration,convergenceValue,ITERATION_TIME, metricValues...

[...]

    60, conv: 2.38023e-05, time: 11.47s, Metric 0: -0.31977848, Metric 1: 0.00062045, Metric 2: 0.00041408, Metric 3: 0.00044147, Metric 4: 0.00044133

  Current level = 2 of 4

    number of iterations = 60

    shrink factors = [4, 4, 4]

    smoothing sigmas = 0.40000001 vox

    required fixed parameters = [74, 68, 45, 7, -79.05253072897736, -80.4645205722302, -42.19026734935695, 0, 2.000002384185791, 2, 2, 1, 0.9987591399204215, -0.017259023951264815, -0.04671516205346462, 0, 0.017233051097196844, 0.9998510403254234, -0.0009587218387751775, 0, 0.04672475120641155, 0.00015248743758484006, 0.9989077907828903, 0, 0, 0, 0, 1]

Iteration,convergenceValue,ITERATION_TIME, metricValues...

[...]

    60, conv: 9.24135e-06, time: 65.69s, Metric 0: -0.31819185, Metric 1: 0.00074039, Metric 2: 0.00042808, Metric 3: 0.00045727, Metric 4: 0.00045587

  Current level = 3 of 4

    number of iterations = 60

    shrink factors = [2, 2, 2]

    smoothing sigmas = 0.20000000 vox

    required fixed parameters = [148, 136, 91, 7, -79.49656622021531, -80.97210390637444, -43.212613787311966, 0, 1.0000011920928955, 1, 1, 1, 0.9987591399204215, -0.017259023951264815, -0.04671516205346462, 0, 0.017233051097196844, 0.9998510403254234, -0.0009587218387751775, 0, 0.04672475120641155, 0.00015248743758484006, 0.9989077907828903, 0, 0, 0, 0, 1]

Iteration,convergenceValue,ITERATION_TIME, metricValues...

[...]

    60, conv: 1.42298e-05, time: 1037.31s, Metric 0: -0.29682542, Metric 1: 0.00083272, Metric 2: 0.00041738, Metric 3: 0.00045008, Metric 4: 0.00044593

  Current level = 4 of 4

    number of iterations = 60

    shrink factors = [1, 1, 1]

    smoothing sigmas = 0.00000000 vox

    required fixed parameters = [296, 272, 182, 7, -79.73026275634766, -81.22613525390625, -43.47406005859375, 0, 0.5000005960464478, 0.5, 0.5, 1, 0.9987591399204215, -0.017259023951264815, -0.04671516205346462, 0, 0.017233051097196844, 0.9998510403254234, -0.0009587218387751775, 0, 0.04672475120641155, 0.00015248743758484006, 0.9989077907828903, 0, 0, 0, 0, 1]

Exception caught: 

itk::MemoryAllocationError (0x7f28300437e0)

Location: "unknown" 

File: /stbb_home/irfanogo/Desktop/codes/other_codes/ANTS_05_23_2014/antsbin/InsightToolkit-4.12.0/Modules/Core/Common/include/itkImportImageContainer.hxx

Line: 199

Description: Failed to allocate memory for image.

Starting DWIs based fine tuning...

[...]

Transforming volume: 0

Transforming volume: 1

Transforming volume: 2

Enter code here...