[MINC-users] nonlinear registration bombs with 0.5 mm isotropic voxels
Claude LEPAGE
claude at bic.mni.mcgill.ca
Fri May 29 11:57:28 EDT 2009
Patrick,
I could not reproduce your error.
I tried with mni_autoreg 0.99.3 and 0.99.5 (internal cvs version)
on both 32 and 64 bits architectures. I also ran 0.99.3 and 0.99.5
32-bits through valgrind successfully. I would say that the code is
probably safe. Perhaps, as Andrew suggested, you ran out of memory.
I know that many minc applications do not check the return status of
memory allocation and keep on going as if memory had been allocated.
bye
Claude
> Dear MINCphilic colleagues,
>
> I am experiencing a problem with a nonlinear fit of 0.5 mm isotropic
> volumes. The script exits at the first iteration of the first fit.
> I've placed everything I'm using here:
>
> /data/scratch/scratch2/patrick
>
> and the command I'm using is:
>
> ./04mm_NLfit.pl -source_mask 0.5mm_lsq12_subject_004_t1_nuc_mask.mnc
> -target_mask 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
> 0.5mm_lsq12_subject_004_t1_nuc.mnc
> 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI.mnc nl.xfm
>
>
> The resulting minctracc debug output looks like this:
>
> ===== Debugging information from minctracc =====
> Data filename =
> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_8_blur.mnc
> Model filename =
> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_8_blur.mnc
> Data mask filename = 0.5mm_lsq12_subject_004_t1_nuc_mask.mnc
> Model mask filename = 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
> Input xform name =
> Output filename =
> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_0.xfm
> Step size = 16.000000 16.000000 16.000000
> Sub-lattice dia = 48.000000 48.000000 48.000000
> Objective function = cross correlation (threshold = 0.000000 0.000000)
> Transform linear = TRUE
> Transform inverted? = FALSE
> Transform type = 9
> Transform matrix = 1.0000 0.0000 0.0000 0.0000
> 0.0000 1.0000 0.0000 0.0000
> 0.0000 0.0000 1.0000 0.0000
> Transform center = 0.000 0.000 0.000
> Transform rotation = 0.000 0.000 0.000
>
> Transform trans = 0.000 0.000 0.000
> Transform scale = 1.000 1.000 1.000
>
> This run will use sub-lattice correlation (type 5) between the two input
> vols.
> Source volume size: 361 by 433 by 361
> Source voxel = 0.500 0.500 0.500
> min/max value= 0.001 80.845
> min/max voxel= 0.000 4095.000
>
> Target volume size: 361 by 433 by 361
> Target voxel = 0.500 0.500 0.500
> min/max value= -0.000 65.645
> min/max voxel= -32768.000 32767.000
>
>
> using input transformation to get initial parameters:
> Center of rot/scale not forced, will be set to : 0.000000 0.000000
> 0.000000
> AFTER init_params()
> Transform matrix = 1.0000 0.0000 0.0000 0.0000
> 0.0000 1.0000 0.0000 0.0000
> 0.0000 0.0000 1.0000 0.0000
>
> Transform center = 0.000 0.000 0.000
> Transform rotations = 0.000 0.000 0.000
> Transform trans = 0.000 0.000 0.000
> Transform scale = 1.000 1.000 1.000
> Transform shear = 0.000 0.000 0.000
>
> In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
> slice lim 0 9
> row lim 1 12
> col lim 1 9
> thresh = 0.00000 0.00000
> In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
> Target volume is smallest
> Lattice step size = 16.000 16.000 16.000
> Lattice start = -64.000 -106.000 -62.000
> Lattice count = 9 12 10
>
> In append_new_default_deformation_field...
> in append new def, the start is: -64.000 -106.000 -62.000
> in append_new_default_deformation_field:
> count_extended= 3 15 17 14
> point: -104.000 -146.000 -102.000
> start: -104.000 -146.000 -102.000
> wstrt: -104.000 -146.000 -102.000
> voxel: 0.000 0.000 0.000
> dirs: 1.000 0.000 0.000
> dirs: 0.000 1.000 0.000
> dirs: 0.000 0.000 1.000
> There are 1 feature pairs
> 0: [5] [1.00000]
> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_8_blur.mnc
> <->
> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_8_blur.mnc
> A sub-lattice is needed for at least one feature
> Sub-lattice dia = 48.000000 48.000000 48.000000
> orig transform is 2 long
> all_until_last is 1 long
> inside do_nonlinear: thresh: 0.0000 0.0000
> 443 433 -> 0.00440087
>
>
> Debug info from do_nonlinear_optimization---------------
> Initial corr = 0.004401
> Source vol threshold = 0.000000
> Target vol threshold = 0.000000
> Iteration limit = 20
> Iteration weight = 1.000000
> xyzv = 3 2 1 0
> number_dimensions = 3
> num_of_dims_to_opt = 3
> smoothing_weight = 1.000000
> loop = (1 13) (1 16) (1 14)
> current_def_vector = 0.000000 0.000000 0.000000
>
> Fitting STRATEGY ----------
> This fit will use local simplex optimization and
> Simplex radius = 32.00 (voxels) or 16.00(mm)
> global smoothing.
> The similarity function will be evaluated using tri-linear interpolation
> on a ellipsoidal sub-lattice with a radii of
> 6 nodes across the diameter
> 96.00, 96.00, 96.00 (data voxels),
> 48.00 48.00 48.00 (mm) width
> 19.20 19.20 19.20 (data voxels) per node
> 9.60 9.60 9.60 (mm) per node
> -----------------------
> Iteration 1 of 20
> Died at ./04mm_NLfit.pl line 285.
>
>
> A colleague has tracked down the following (in case it helps): minctracc
> aborts in function "go_get_samples_with_offset" (sub_lattice.c:612) when
> it attempts to make use of a null/zero Volume pointer (pointer
> "sshort_ptr", line 612). The indices themselves appear to be within range.
>
> Any and all help will be greatly appreciated. Cheers.
>
> Patrick
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
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