[slicer-users] Plastimatch error

Zhang, Yi Yi.Zhang2 at ucsf.edu
Fri Mar 4 17:23:29 EST 2011


Thank you Steve and Greg for all of your help!
Plastimatch is running well with the new release.

Vickie
On Mar 2, 2011, at 6:10 AM, Steve Pieper wrote:

> Hi Vickie -
>
> The slicer nightly builds are made with ubuntu 8.04, but apparently
> those binaries don't run on centos/redhat 5.5.
>
> You can try the near-final versions of the next release here:
>
> http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/
>
> The plastimatch extension should work with those builds (linux or mac),
> but let us know if it doesn't.
>
> -Steve
>
> On 03/01/2011 07:55 PM, Zhang, Yi wrote:
>> Hi Greg,
>>
>> I tried to upgrade Slicer to 2010-11-3 on our linux network. However, I got an error running Slicer3 - "/usr/lib64/libstdc++.so.6: version 'GLIBCXX_3.4.9' not found"
>> So I think our network does not have the updated GLIBC to run most updated Slicer3.
>> I downloaded the mac version of Slicer3 to my mac computer - Slicer3-3.6.2-2010-11-03-darwin-x86 and Slicer3 is running. I cannot locate plastimatch from the extension manager (path: http://ext.slicer.org/ext/Slicer-3-6/15432-darwin-x86).
>>
>> Do you have a working plastimatch on a mac version of Slicer3? If you do, what is the path to find that plastimatch?
>>
>> Thanks,
>> Vickie
>>
>> On Feb 25, 2011, at 6:25 AM, Gregory Sharp wrote:
>>
>>>
>>> Hi Vickie,
>>>
>>> Oops, my bad.  You are right.  That version is not compatible.
>>>
>>> Would you consider upgrading your Slicer version to 2010-11-03?
>>>
>>> Greg
>>>
>>>
>>> On Thu, 24 Feb 2011 20:11:31 -0800
>>> "Zhang, Yi"<Yi.Zhang2 at ucsf.edu>  wrote:
>>>
>>>> Hi Greg,
>>>>
>>>> After downloading plastimatch from
>>>> http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/<http://ext.slicer.org/ext/Slicer-3-6/16102-linux-x86_64/>
>>>> <http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/>I don't see
>>>> plastimatch under Modules anymore. It seems to have disappeared from
>>>> Slicer3. Any ideas?
>>>>
>>>> Vickie
>>>> On Feb 24, 2011, at 6:30 PM, Sharp, Gregory C. wrote:
>>>>
>>>>
>>>> Hi Vickie,
>>>>
>>>> Thanks for your patience and persistence!
>>>>
>>>> You have hit a bug in plastimatch which thankfully is already fixed.
>>>> Can you try to update your plastimatch?  You will need to point the
>>>> extensions "Where to search" URL to a different location:
>>>>
>>>> For 32-bit linux it is here:
>>>>
>>>> http://ext.slicer.org/ext/Slicer-3-6/16108%2dlinux%2dx86/
>>>>
>>>> For 64-bit linux it is here:
>>>>
>>>> http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/
>>>>
>>>> Greg
>>>>
>>>> -----Original Message-----
>>>> From: Zhang, Yi [mailto:Yi.Zhang2 at ucsf.edu]
>>>> Sent: Thu 2/24/2011 6:24 PM
>>>> To: Sharp, Gregory C.
>>>> Cc: slicer-users at bwh.harvard.edu
>>>> Subject: Re: [slicer-users] Plastimatch error
>>>>
>>>> Hi Greg,
>>>>
>>>> Sorry I was out of the office last few days.
>>>> I tried 5 or 10 mm grid size, but still I'm getting errors.
>>>> again, both volumes are:
>>>> Image matrix: 256 by 256 by 22
>>>> Image resolution: 0.15625 by 0.15625 by 1.25mm
>>>>
>>>> Stage 1:
>>>> subsampling rate: 1,1,1
>>>> Grid size (mm): 10
>>>> Max iterations: 30
>>>>
>>>> result: completed with errors: (B-spline deformable registration), 20.91s
>>>> Error log:
>>>> ERROR: In
>>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
>>>> ic.cxx, line 1522
>>>> vtkCommandLineModuleLogic (0x1270af00): B-spline deformable registration
>>>> completed with errors
>>>> "Information":
>>>> B-spline deformable registration standard output:
>>>>
>>>> fixed
>>>> image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeC.nrrd
>>>> Loading fixed image...
>>>> done!
>>>> moving
>>>> image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeB.nrrd
>>>> Loading moving image...
>>>> done!
>>>> [1] xf_in->m_type = 0, xf_out->m_type = 0
>>>> Converting fixed
>>>> Converting moving
>>>> Done.
>>>> SUBSAMPLE: (1 1 1), (1 1 1)
>>>> moving_ss size = 256 256 22
>>>> fixed_ss size = 256 256 22
>>>> bspline_xform_initialize
>>>> rdims = (4,4,3)
>>>> vox_per_rgn = (64,64,8)
>>>> cdims = (7 7 6)
>>>> xform_any_to_gpuit_bsp complete
>>>> BSPLINE PARMS
>>>> max_its = 30
>>>> BSPLINE XFORM HEADER
>>>> vox_per_rgn = 64 64 8
>>>> roi_offset = 0 0 0
>>>> roi_dim = 256 256 22
>>>> Setting NMAX, MMAX = 882 49
>>>> START
>>>> RUNNING THE L-BFGS-B CODE
>>>>
>>>>          * * *
>>>>
>>>> Machine precision = 2.220E-16
>>>> N =  882    M =  49
>>>> This problem is unconstrained.
>>>> MSE[   0] 172793.406 NV 1430550 GM  3440.164 GN 40055.410 [    0.699 secs]
>>>>                   CMIN   0.00 CAVG   0.00 CMAX   0.00
>>>> MSE[   1] 168788.625 NV 1436510 GM -14022.742 GN 44458.961 [    0.701 secs]
>>>>                   CMIN  -0.26 CAVG  -0.00 CMAX   0.27
>>>> MSE[   2] 156002.094 NV 1427438 GM -9776.679 GN 38473.344 [    0.721 secs]
>>>>                   CMIN  -1.29 CAVG  -0.01 CMAX   1.36
>>>> MSE[   3] 113203.945 NV 1376563 GM -1506.240 GN 36962.977 [    0.701 secs]
>>>>                   CMIN  -5.42 CAVG  -0.02 CMAX   5.73
>>>> MSE[   4] 182364.469 NV 1221763 GM  8802.257 GN 44880.477 [    0.665 secs]
>>>>                   CMIN -16.33 CAVG  -0.06 CMAX  23.58
>>>> MSE[   5] 88962.250 NV 1334618 GM  2365.741 GN 29213.508 [    0.686 secs]
>>>>                   CMIN  -8.32 CAVG  -0.03 CMAX  10.47
>>>> MSE[   6] 74965.664 NV 1301347 GM -3784.107 GN 22351.080 [    0.680 secs]
>>>>                   CMIN  -8.87 CAVG  -0.05 CMAX  11.16
>>>> MSE[   7] 68752.648 NV 1261210 GM -9005.963 GN 20776.543 [    0.672 secs]
>>>>                   CMIN  -9.90 CAVG  -0.05 CMAX  10.98
>>>> MSE[   8] 62334.117 NV 1253569 GM   -84.478 GN 13559.529 [    0.670 secs]
>>>>                   CMIN -10.70 CAVG  -0.03 CMAX  11.15
>>>> MSE[   9] 59037.574 NV 1242716 GM  9142.486 GN 15676.164 [    0.669 secs]
>>>>                   CMIN -11.83 CAVG  -0.02 CMAX  11.41
>>>> MSE[  10] 56116.086 NV 1223911 GM  5785.482 GN 11916.921 [    0.665 secs]
>>>>                   CMIN -13.08 CAVG  -0.03 CMAX  12.40
>>>> MSE[  11] 51500.602 NV 1178880 GM  1053.619 GN 11454.988 [    0.656 secs]
>>>>                   CMIN -16.59 CAVG  -0.05 CMAX  14.58
>>>> MSE[  12] 48438.137 NV 1149236 GM -3097.842 GN  9308.528 [    0.649 secs]
>>>>                   CMIN -19.33 CAVG  -0.08 CMAX  16.23
>>>> MSE[  13] 45976.199 NV 1122297 GM -1455.273 GN  7629.981 [    0.644 secs]
>>>>                   CMIN -22.45 CAVG  -0.09 CMAX  17.95
>>>> MSE[  14] 44144.320 NV 1106619 GM -1121.861 GN  6836.752 [    0.641 secs]
>>>>                   CMIN -24.13 CAVG  -0.09 CMAX  19.08
>>>> MSE[  15] 42542.715 NV 1052552 GM -2756.149 GN  8741.547 [    0.630 secs]
>>>>                   CMIN -30.40 CAVG  -0.08 CMAX  25.25
>>>> MSE[  16] 40959.645 NV 1040040 GM  2106.021 GN 11453.347 [    0.627 secs]
>>>>                   CMIN -31.82 CAVG  -0.05 CMAX  27.37
>>>> MSE[  17] 38835.320 NV 1047948 GM   171.968 GN  5861.133 [    0.629 secs]
>>>>                   CMIN -30.59 CAVG  -0.05 CMAX  26.64
>>>> MSE[  18] 38289.160 NV 1033359 GM  2835.816 GN  6007.721 [    0.634 secs]
>>>>                   CMIN -31.34 CAVG  -0.05 CMAX  28.26
>>>> MSE[  19] 37757.949 NV 1022548 GM   764.146 GN  5460.470 [    0.624 secs]
>>>>                   CMIN -32.10 CAVG  -0.05 CMAX  29.80
>>>> MSE[  20] 36572.082 NV 990523 GM  -990.091 GN  5187.105 [    0.618 secs]
>>>>                   CMIN -34.10 CAVG  -0.06 CMAX  34.08
>>>> MSE[  21] 35282.254 NV 952616 GM -3800.624 GN  7294.177 [    0.618 secs]
>>>>                   CMIN -35.25 CAVG  -0.07 CMAX  38.78
>>>> MSE[  22] 33919.004 NV 938209 GM  -242.454 GN  5740.723 [    0.608 secs]
>>>>                   CMIN -33.92 CAVG  -0.08 CMAX  40.26
>>>> MSE[  23] 33370.039 NV 916397 GM  1086.198 GN  5384.354 [    0.603 secs]
>>>>                   CMIN -34.06 CAVG  -0.07 CMAX  42.59
>>>> MSE[  24] 32082.525 NV 927453 GM   492.501 GN  5629.464 [    0.605 secs]
>>>>                   CMIN -31.95 CAVG  -0.07 CMAX  41.66
>>>> MSE[  25] 31317.986 NV 923391 GM   430.064 GN  3504.146 [    0.604 secs]
>>>>                   CMIN -31.63 CAVG  -0.07 CMAX  42.50
>>>> MSE[  26] 30691.617 NV 920224 GM    70.180 GN  3819.907 [    0.610 secs]
>>>>                   CMIN -31.26 CAVG  -0.07 CMAX  43.41
>>>> MSE[  27] 30035.088 NV 914436 GM  -474.841 GN  4630.180 [    0.603 secs]
>>>>                   CMIN -30.58 CAVG  -0.06 CMAX  44.40
>>>> MSE[  28] 29283.193 NV 902584 GM  -565.189 GN  6579.526 [    0.600 secs]
>>>>                   CMIN -29.99 CAVG  -0.06 CMAX  46.43
>>>> MSE[  29] 28504.350 NV 899740 GM   403.089 GN  5322.814 [    0.599 secs]
>>>>                   CMIN -30.24 CAVG  -0.06 CMAX  47.21
>>>> MSE[  30] 27685.469 NV 880915 GM  -360.044 GN  6465.846 [    0.595 secs]
>>>>                   CMIN -32.59 CAVG  -0.06 CMAX  49.30
>>>> [2] xf_out->m_type = 8, xf_in->m_type = 0
>>>> Warping...
>>>> Running: plm_warp_native
>>>> Converting input image...
>>>> Converting xform...
>>>> bspline_xform_initialize
>>>> rdims = (4,4,3)
>>>> vox_per_rgn = (64,64,8)
>>>> cdims = (7 7 6)
>>>> Input pih
>>>> Origin
>>>> [-20, -20, -13]
>>>> Spacing
>>>> [0.15625, 0.15625, 1.25]
>>>> Region
>>>> ImageRegion (0x7fffd0b054d0)
>>>> Dimension: 3
>>>> Index: [0, 0, 0]
>>>> Size: [256, 256, 22]
>>>> Running: gpuit_bsp_to_itk_bsp_raw
>>>> Setting bsp_spacing
>>>> [10, 10, 10]
>>>> Setting bsp_origin
>>>> [-30, -30, -23]
>>>> Setting bsp_region
>>>> ImageRegion (0x7fffd0b04ee0)
>>>> Dimension: 3
>>>> Index: [0, 0, 0]
>>>> Size: [7, 7, 6]
>>>> Setting bsp_direction = 1 0 0 0 1 0 0 0 1
>>>> Running: xform_itk_bsp_to_itk_bsp
>>>> Setting bsp_spacing
>>>> [10, 10, 10]
>>>> Setting bsp_origin
>>>> [-30, -30, -23]
>>>> Setting bsp_region
>>>> ImageRegion (0x7fffd0b04c30)
>>>> Dimension: 3
>>>> Index: [0, 0, 0]
>>>> Size: [7, 7, 6]
>>>> Setting bsp_direction = 1 0 0 0 1 0 0 0 1
>>>> Completed: xform_itk_bsp_to_itk_bsp
>>>> Creating output volume...
>>>> Unhandled image type in Plm_image::convert (14 ->  4)
>>>>
>>>>
>>>> Thanks,
>>>> Vickie
>>>> On Feb 21, 2011, at 9:04 AM, Sharp, Gregory C. wrote:
>>>>
>>>>
>>>> Hi Vickie,
>>>>
>>>> Please try setting the "Grid Size" parameter to something
>>>> smaller than the image size.  For a smoother deformation,
>>>> you may try 10 mm or 20 mm.  For a wigglier deformation, you
>>>> may try something like 1 mm or 5 mm.
>>>>
>>>> Greg
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Zhang, Yi [mailto:Yi.Zhang2 at ucsf.edu]
>>>> Sent: Sun 2/20/2011 10:28 PM
>>>> To: Sharp, Gregory C.
>>>> Cc: slicer-users at bwh.harvard.edu
>>>> Subject: Re: [slicer-users] Plastimatch error
>>>>
>>>> Image matrix: 256 by 256 by 22
>>>> image resolution: 0.15625 by 0.15625 by 1.25mm
>>>> FOV: 40 by 40 by 27.5 mm
>>>> Thanks,
>>>> Vickie
>>>> On Feb 20, 2011, at 7:00 PM, Sharp, Gregory C. wrote:
>>>>
>>>>
>>>> Hi Vickie,
>>>>
>>>> This is very helpful.  It looks like the registration code
>>>> is running out of memory building the lookup table.
>>>>
>>>> I think this can be solved by changing the grid spacing.
>>>> Can you tell me your image resolution and voxel spacing?
>>>> Then I will suggest some modified settings.
>>>>
>>>> Greg
>>>>
>>>> -----Original Message-----
>>>> From: Zhang, Yi [mailto:Yi.Zhang2 at ucsf.edu]
>>>> Sent: Fri 2/18/2011 4:54 PM
>>>> To: Sharp, Gregory C.
>>>> Cc: slicer-users at bwh.harvard.edu
>>>> Subject: Re: [slicer-users] Plastimatch error
>>>>
>>>> Hi Greg,
>>>>
>>>> I downloaded Slicer3-3.6-2010-06-10-linux-x86_64 to our linux network. And
>>>> installed Plastimatch from
>>>> http://ext.slicer.org/ext/Slicer-3-6/13744-linux-x86_64
>>>> Tested with 2 3D images.
>>>> It ran for 75.42 secs and completed with errors.
>>>>
>>>> ERROR: In
>>>>
>>>>
>>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
>>>> ic.cxx, line 1522
>>>> vtkCommandLineModuleLogic (0x1d5d97a0): B-spline deformable registration
>>>> completed with errors
>>>>
>>>> I have two 3D mask images in nrrd format, same resolution, same matrix size
>>>> and
>>>> FOV.
>>>> Using Plastimatch B-spline Registration, I left stage 0 and stage 2
>>>> unchecked.
>>>> For stage 1, I put subsampling rate = [1,1,1], Grid size = 100, max
>>>> iterations
>>>> =
>>>> 50
>>>> Afer 75.42 seconds, it completed with following error:
>>>>
>>>> Looks like the linux is working better, but still gives errors. Any
>>>> suggestions?
>>>>
>>>> Thanks,
>>>> Vickie
>>>>
>>>> FYI: output from "Information"
>>>>
>>>> B-spline deformable registration standard output:
>>>>
>>>> fixed
>>>> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeC.nrrd
>>>> Loading fixed image...
>>>> done!
>>>> moving
>>>> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeB.nrrd
>>>> Loading moving image...
>>>> done!
>>>> [1] xf_in->m_type = 0, xf_out->m_type = 0
>>>> Converting fixed
>>>> Converting moving
>>>> Done.
>>>> SUBSAMPLE: (1 1 1), (1 1 1)
>>>> moving_ss size = 256 256 22
>>>> fixed_ss size = 256 256 22
>>>> bspline_xform_initialize
>>>> rdims = (1,1,1)
>>>> vox_per_rgn = (640,640,80)
>>>> cdims = (4 4 4)
>>>> xform_any_to_gpuit_bsp complete
>>>> BSPLINE PARMS
>>>> max_its = 50
>>>> BSPLINE XFORM HEADER
>>>> vox_per_rgn = 640 640 80
>>>> roi_offset = 0 0 0
>>>> roi_dim = 256 256 22
>>>> Setting NMAX, MMAX = 192 33
>>>> START
>>>> RUNNING THE L-BFGS-B CODE
>>>>
>>>>        * * *
>>>>
>>>> Machine precision = 2.220E-16
>>>> N =  192    M =  33
>>>> This problem is unconstrained.
>>>> MSE[   0] 172793.406 NV 1430550 GM  3439.737 GN 30124.119 [   10.775 secs]
>>>>                 CMIN   0.00 CAVG   0.00 CMAX   0.00
>>>> MSE[   1] 168275.266 NV 1424940 GM -5014.567 GN 30481.576 [    0.820 secs]
>>>>                 CMIN  -0.47 CAVG  -0.00 CMAX   0.55
>>>> MSE[   2] 157821.125 NV 1364025 GM   490.165 GN 10444.228 [    0.824 secs]
>>>>                 CMIN  -2.33 CAVG  -0.01 CMAX   2.75
>>>> MSE[   3] 150639.672 NV 1322945 GM -3168.723 GN  8878.263 [    0.819 secs]
>>>>                 CMIN  -3.54 CAVG  -0.02 CMAX   4.65
>>>> MSE[   4] 188038.469 NV 1104705 GM  5709.269 GN 35672.590 [    0.779 secs]
>>>>                 CMIN  -8.39 CAVG  -0.02 CMAX  12.27
>>>> MSE[   5] 148842.766 NV 1243158 GM  1997.787 GN 20606.512 [    0.810 secs]
>>>>                 CMIN  -4.44 CAVG  -0.02 CMAX   6.07
>>>> MSE[   6] 148750.625 NV 1209877 GM  2647.233 GN 16888.412 [    0.790 secs]
>>>>                 CMIN  -5.12 CAVG  -0.02 CMAX   7.14
>>>> MSE[   7] 806886.812 NV 381837 GM 21044.473 GN 23951.367 [    0.614 secs]
>>>>                 CMIN -27.43 CAVG  -0.06 CMAX  45.42
>>>> MSE[   8] 152320.859 NV 1185717 GM  5175.555 GN 16294.637 [    0.780 secs]
>>>>                 CMIN  -5.81 CAVG  -0.02 CMAX   8.33
>>>> MSE[   9] 148912.469 NV 1207340 GM  1072.352 GN 17781.539 [    0.781 secs]
>>>>                 CMIN  -5.21 CAVG  -0.02 CMAX   7.29
>>>> MSE[  10] 148732.609 NV 1209789 GM  3026.238 GN 16650.699 [    0.782 secs]
>>>>                 CMIN  -5.14 CAVG  -0.02 CMAX   7.16
>>>> MSE[  11] 148842.719 NV 1208203 GM  2533.625 GN 16642.928 [    0.780 secs]
>>>>                 CMIN  -5.18 CAVG  -0.02 CMAX   7.25
>>>> MSE[  12] 148723.188 NV 1209753 GM  3064.563 GN 16639.996 [    0.781 secs]
>>>>                 CMIN  -5.14 CAVG  -0.02 CMAX   7.18
>>>> MSE[  13] 148801.906 NV 1208722 GM  2787.533 GN 16551.098 [    0.780 secs]
>>>>                 CMIN  -5.17 CAVG  -0.02 CMAX   7.22
>>>> MSE[  14] 148718.281 NV 1209738 GM  3013.684 GN 16662.023 [    0.780 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.18
>>>> MSE[  15] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.785 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  16] 148759.312 NV 1209209 GM  2952.867 GN 16575.090 [    0.783 secs]
>>>>                 CMIN  -5.16 CAVG  -0.02 CMAX   7.20
>>>> MSE[  17] 148717.328 NV 1209686 GM  3028.778 GN 16613.072 [    0.787 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  18] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.779 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  19] 150613.188 NV 1190233 GM   995.946 GN 13185.175 [    0.783 secs]
>>>>                 CMIN  -5.87 CAVG  -0.04 CMAX   8.12
>>>> MSE[  20] 148911.750 NV 1206059 GM   596.928 GN 16508.850 [    0.790 secs]
>>>>                 CMIN  -5.29 CAVG  -0.02 CMAX   7.37
>>>> MSE[  21] 148749.172 NV 1208980 GM  2882.243 GN 16270.943 [    0.847 secs]
>>>>                 CMIN  -5.17 CAVG  -0.02 CMAX   7.22
>>>> MSE[  22] 148719.094 NV 1209605 GM  2989.419 GN 16580.570 [    0.797 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  23] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.834 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  24] 148717.031 NV 1209645 GM  2999.337 GN 16592.098 [    0.798 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  25] 148714.031 NV 1209707 GM  3021.097 GN 16605.896 [    0.786 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  26] 148713.828 NV 1209715 GM  3023.048 GN 16609.420 [    0.789 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  27] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.775 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  28] 175370.141 NV 1071035 GM  -907.450 GN 33266.391 [    0.749 secs]
>>>>                 CMIN  -8.56 CAVG  -0.09 CMAX  11.31
>>>> MSE[  29] 149951.703 NV 1198289 GM   410.754 GN 15046.626 [    0.774 secs]
>>>>                 CMIN  -5.63 CAVG  -0.03 CMAX   7.77
>>>> MSE[  30] 148812.062 NV 1207861 GM  1381.749 GN 16895.891 [    0.772 secs]
>>>>                 CMIN  -5.23 CAVG  -0.02 CMAX   7.28
>>>> MSE[  31] 148737.641 NV 1209338 GM  2954.447 GN 16500.389 [    0.773 secs]
>>>>                 CMIN  -5.16 CAVG  -0.02 CMAX   7.20
>>>> MSE[  32] 148717.484 NV 1209658 GM  2991.898 GN 16609.189 [    0.773 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  33] 148713.969 NV 1209711 GM  3016.083 GN 16610.049 [    0.772 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  34] 148713.906 NV 1209715 GM  3019.795 GN 16611.596 [    0.772 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  35] 148713.750 NV 1209717 GM  3013.334 GN 16615.154 [    0.779 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  36] 148713.812 NV 1209716 GM  3019.594 GN 16611.320 [    0.775 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  37] 148713.734 NV 1209717 GM  3015.496 GN 16613.883 [    0.775 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  38] 148713.703 NV 1209717 GM  3019.348 GN 16611.369 [    0.780 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  39] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.792 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  40] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.785 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  41] 149230.156 NV 1202567 GM -3212.984 GN 13317.635 [    0.787 secs]
>>>>                 CMIN  -5.63 CAVG  -0.04 CMAX   7.56
>>>> MSE[  42] 148573.141 NV 1209045 GM  1713.927 GN 15354.268 [    0.769 secs]
>>>>                 CMIN  -5.26 CAVG  -0.02 CMAX   7.27
>>>> MSE[  43] 143860.938 NV 1209402 GM  -855.199 GN  6535.604 [    0.779 secs]
>>>>                 CMIN  -5.11 CAVG  -0.04 CMAX   7.84
>>>> MSE[  44] 139446.422 NV 1215427 GM -1688.968 GN  8863.167 [    0.781 secs]
>>>>                 CMIN  -5.03 CAVG  -0.05 CMAX   8.18
>>>> MSE[  45] 127585.609 NV 1177313 GM  2248.406 GN  6065.925 [    0.775 secs]
>>>>                 CMIN  -7.75 CAVG  -0.06 CMAX   9.52
>>>> MSE[  46] 127429.797 NV 985327 GM 21602.986 GN 23426.008 [    0.740 secs]
>>>>                 CMIN -19.57 CAVG  -0.14 CMAX  15.94
>>>> MSE[  47] 118871.992 NV 1057706 GM 15481.925 GN 19304.348 [    0.762 secs]
>>>>                 CMIN -14.77 CAVG  -0.12 CMAX  13.34
>>>> MSE[  48] 213189.203 NV 1073180 GM -12869.133 GN 23120.221 [    0.754 secs]
>>>>                 CMIN -10.03 CAVG   0.00 CMAX  11.79
>>>> MSE[  49] 116845.352 NV 1075250 GM 11625.675 GN 14186.798 [    0.771 secs]
>>>>                 CMIN -12.47 CAVG  -0.11 CMAX  12.07
>>>> MSE[  50] 115312.266 NV 1067161 GM 10351.102 GN 15636.233 [    0.764 secs]
>>>>                 CMIN -13.62 CAVG  -0.12 CMAX  12.84
>>>> [2] xf_out->m_type = 8, xf_in->m_type = 0
>>>> Warping...
>>>> Running: plm_warp_native
>>>> Converting input image...
>>>> Converting xform...
>>>> bspline_xform_initialize
>>>> Error allocating memory for q_lut
>>>>
>>>> On Feb 18, 2011, at 10:44 AM, Gregory Sharp wrote:
>>>>
>>>>
>>>> Hi Vickie,
>>>>
>>>> Unfortunately I couldn't reproduce the problem.  You are using a good
>>>> configuration of versions which is supposed to work.
>>>>
>>>> We should test if the problem is with Parallels.  Can you please try
>>>> downloading and running another extension, such as ExampleCommandLine?
>>>> (By the way, why do you run Slicer on Parallels instead of the OSX native
>>>> version?)
>>>>
>>>> Also, can you tell me if there is any output in the "standard output"
>>>> part of the error log?
>>>>
>>>> An alternative route is to run plastimatch independent of Slicer, then
>>>> loading the results into Slicer for further analysis.  Let me know if you
>>>> like to pursue that route and I can walk you through.
>>>>
>>>> Greg
>>>>
>>>>
>>>> On Thu, 17 Feb 2011 10:22:33 -0800
>>>> "Zhang, Yi"<Yi.Zhang2 at ucsf.edu>  wrote:
>>>>
>>>> Sorry,
>>>> OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
>>>> using the Parallels Desktop since I don't own a PC. (do you think that
>>>> could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
>>>> extension version:
>>>>
>>>>
>>>>
>>>> http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010
>>>> -06-10-win32
>>>>
>>>> Actually, not only B-spline, but other two functionalities give me the same
>>>> error - DICOM/DICOM RT import and landmark deformable registration.
>>>>
>>>> Thanks,
>>>> Vickie
>>>> On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:
>>>>
>>>>
>>>> Hi Vickie,
>>>>
>>>> Can you please tell me your OS, Slicer Version, and
>>>> extension version (extension URL)?
>>>>
>>>> Thank you,
>>>> Greg
>>>>
>>>> -----Original Message-----
>>>> From: slicer-users-bounces at bwh.harvard.edu
>>>> [mailto:slicer-users-bounces at bwh.harvard.edu] On Behalf Of Zhang, Yi
>>>> Sent: Thursday, February 17, 2011 12:26 AM
>>>> To: slicer-users at bwh.harvard.edu
>>>> Subject: [slicer-users] Plastimatch error
>>>>
>>>> Hi,
>>>>
>>>> I have encountered following error while trying to peform B-spline
>>>> deformable registration on Plastmatch:
>>>>
>>>> ERROR: In
>>>> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
>>>> line 1575
>>>> vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
>>>> process was null when state was queried, result (1) = Error.
>>>>
>>>> Please help.
>>>> Thanks!
>>>> Vickie
>>>>
>>>> --
>>>> Greg Sharp, PhD
>>>> Department of Radiation Oncology
>>>> Massachusetts General Hospital
>>>>
>>>>
>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to whom it is
>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>> e-mail contains patient information, please contact the Partners Compliance
>>>> HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>>>> error
>>>> but does not contain patient information, please contact the sender and
>>>> properly
>>>> dispose of the e-mail.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Greg Sharp, PhD
>>> Department of Radiation Oncology
>>> Massachusetts General Hospital
>>
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