[MINC-users] nu_correct (volume_stats) assertion failed

[Burt Crépeault]

Hi all,

Can't wait to get this OS X 64-bit build going... Man this is tough...
(sigh)

Ok, so this time, it's nu_correct that doesn't run, giving an Assertion
failed at line 32 in file templates/Pool.cc:

neon:Darwin:# nu_correct -clobber -verbose -mapping_dir
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/  -iterations 100
-shrink 3 -fwhm 0.1 -distance 100
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.\[mnc.rsh\]\[mnc.dns\].Br.80_p2.mnc.gz
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.\[mnc.rsh\]\[mnc.dns\]\[mnc.nuc\].Br.70_p2.mnc

[nu_correct] [ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:56]
/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/bin/nu_estimate_np_and_em -parzen
-log -sharpen 0.1 0.01 -iterations 100 -stop 0.001 -shrink 3 -auto_mask
-nonotify -b_spline 1.0e-7 -distance 100 -verbose -execute -clobber
-nokeeptmp -tmpdir /var/tmp/nu_correct_39946/
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns][mnc.nuc].Br.70_p2.imp

Uncorrected volume (input):
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz
Intensity mapping (output):
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns][mnc.nuc].Br.70_p2.imp

# Start of NU estimation algorithm
[nu_estimate_np_and_em]
[ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:56]
/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/bin/mincresample -clobber -verbose
-nearest_neighbour -nelements 61 86 86 -step 3 3 3
'/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz'
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc'
Transforming
slices:......................................................................................Done

[nu_estimate_np_and_em]
[ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:58] /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/bin/mincmath
-clobber -verbose -clamp -const2 1 1.7e+308
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc'
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns][mnc.nuc].Br.70_p2_log.mnc.temp'
Processing:......................................................................................Done

[nu_estimate_np_and_em]
[ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:58]
/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/bin/mincmath -clobber -verbose
-zero -log
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns][mnc.nuc].Br.70_p2_log.mnc.temp'
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns][mnc.nuc].Br.70_p2_log.mnc'
Processing:......................................................................................Done

[nu_estimate_np_and_em]
[ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:58] /bin/rm
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns][mnc.nuc].Br.70_p2_log.mnc.temp'

[nu_estimate_np_and_em]
[ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:58] /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/bin/mincinfo
-attvalue xspace:spacetype -attvalue yspace:spacetype -attvalue
zspace:spacetype
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc'

[nu_estimate_np_and_em]
[ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:58]
/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/bin/volume_stats -quiet -biModalT
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc'
Assertion failed at line 32 in file templates/Pool.cc
nu_estimate_np_and_em: crashed while running volume_stats (termination
status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=256)

That last part attemps to run volume_stats so I gave it a try all by itself:

neon:Darwin:# volume_stats
Assertion failed at line 32 in file templates/Pool.cc

I believe that Pool.cc file belongs to EBTKS, I'm using version 1.6.2. I
checked the output generated during its build, no apparent problem there. I
built it again, just to make sure, and did the same for N3. Everything went
well but the failed assertion error persists.

The relevant section of Pool.cc is:

    26    template <class Type>
    27    Pool<Type>::Pool(unsigned nElements)
    28    : _elementSize(sizeof(Type)),
    29      _expansionSize(nElements),
    30      _blocks(_POOL_N_BLOCKS)
    31    {
    32      assert(_elementSize >= sizeof(_Link *));
    33      assert(nElements);
    34      _head = 0;
    35    }
    36

Any ideas?

Thanks again,

Burt.


-------------
Burt Crépeault
Centre de recherche de l'université Laval - Robert-Giffard
2601 de la Canardière, suite F-4400
Québec QC G1J 2G3
418-663-5741, ext 6844