{"action":"created","issue":{"url":"https://api.github.com/repos/stnava/ANTs/issues/389","repository_url":"https://api.github.com/repos/stnava/ANTs","labels_url":"https://api.github.com/repos/stnava/ANTs/issues/389/labels{/name}","comments_url":"https://api.github.com/repos/stnava/ANTs/issues/389/comments","events_url":"https://api.github.com/repos/stnava/ANTs/issues/389/events","html_url":"https://github.com/stnava/ANTs/issues/389","id":191178985,"number":389,"title":"Question about \"a large deformation example\"","user":{"login":"shansiliu","id":18625221,"avatar_url":"https://avatars.githubusercontent.com/u/18625221?v=3","gravatar_id":"","url":"https://api.github.com/users/shansiliu","html_url":"https://github.com/shansiliu","followers_url":"https://api.github.com/users/shansiliu/followers","following_url":"https://api.github.com/users/shansiliu/following{/other_user}","gists_url":"https://api.github.com/users/shansiliu/gists{/gist_id}","starred_url":"https://api.github.com/users/shansiliu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shansiliu/subscriptions","organizations_url":"https://api.github.com/users/shansiliu/orgs","repos_url":"https://api.github.com/users/shansiliu/repos","events_url":"https://api.github.com/users/shansiliu/events{/privacy}","received_events_url":"https://api.github.com/users/shansiliu/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2016-11-23T03:02:39Z","updated_at":"2016-11-23T04:12:19Z","closed_at":null,"body":"Hi, I am new to ANTs, I have tried for one week to run this simple example(http://stnava.github.io/C/) without success. The system reports \"Segmentation Fault\" all the time.\r\n\r\nI'm using the Windows Release version.\r\n\r\nHere is my c_example.sh file:\r\n\r\ndim=2\r\nm=./data/c.nii.gz \r\nf=./data/chalf.nii.gz\r\nits=[1200x1200x100x20x0,0,5]\r\nsmth=8x6x4x2x1vox\r\ndown=8x6x4x2x1\r\n./antsRegistration -d $dim  \\\r\n                        -m demons[ $f,$m, 0.5, 0 ] \\\r\n                        -m meansquares[ $f,$m, 1, 0 ] \\\r\n                        -t TimeVaryingVelocityField[ 2.0, 8, 1,0.0, 0.05,0 ] \\\r\n                        -c $its  \\\r\n                        -s $smth  \\\r\n                        -f $down \\\r\n                       -u 1 \\\r\n                       -o [output/ex_,output/ex_diff.nii.gz,output/ex_diff_inv.nii.gz] \r\n./CreateWarpedGridImage $dim output/ex_0InverseWarp.nii.gz output/grid.nii.gz \r\n./ConvertToJpg output/grid.nii.gz figures/grid.png \r\n./CreateJacobianDeterminantImage 2 output/ex_0Warp.nii.gz output/jac.nii.gz 0 1\r\n./CreateJacobianDeterminantImage 2 output/ex_0InverseWarp.nii.gz output/jac_inv.nii.gz 0 1\r\n\r\nThis is the output of the system:\r\n$ /cygdrive/d/ANTs_2.1.0_Windows/Release/c_example.sh\r\nAll_Command_lines_OK\r\nUsing double precision for computations.\r\n  number of levels = 5\r\n  fixed image: ./data/chalf.nii.gz\r\n  moving image: ./data/c.nii.gz\r\n  fixed image: ./data/chalf.nii.gz\r\n  moving image: ./data/c.nii.gz\r\nDimension = 2\r\nNumber of stages = 1\r\nUse Histogram Matching true\r\nWinsorize image intensities false\r\nLower quantile = 0\r\nUpper quantile = 1\r\nStage 1 State\r\n   Image metric = Demons\r\n     Fixed image = Image (000001BC56DA30A0)\r\n  RTTI typeinfo:   class itk::Image<double,2>\r\n  Reference Count: 2\r\n  Modified Time: 619\r\n  Debug: Off\r\n  Object Name:\r\n  Observers:\r\n    none\r\n  Source: (none)\r\n  Source output name: (none)\r\n  Release Data: Off\r\n  Data Released: False\r\n  Global Release Data: Off\r\n  PipelineMTime: 0\r\n  UpdateMTime: 440\r\n  RealTimeStamp: 0 seconds\r\n  LargestPossibleRegion:\r\n    Dimension: 2\r\n    Index: [0, 0]\r\n    Size: [150, 150]\r\n  BufferedRegion:\r\n    Dimension: 2\r\n    Index: [0, 0]\r\n    Size: [150, 150]\r\n  RequestedRegion:\r\n    Dimension: 2\r\n    Index: [0, 0]\r\n    Size: [150, 150]\r\n  Spacing: [1, 1]\r\n  Origin: [0, 0]\r\n  Direction:\r\n1 0\r\n0 -1\r\n\r\n  IndexToPointMatrix:\r\n1 0\r\n0 -1\r\n\r\n  PointToIndexMatrix:\r\n1 0\r\n0 -1\r\n\r\n  Inverse Direction:\r\n1 0\r\n0 -1\r\n\r\n  PixelContainer:\r\n    ImportImageContainer (000001BC56D77000)\r\n      RTTI typeinfo:   class itk::ImportImageContainer<unsigned long,double>\r\n      Reference Count: 1\r\n      Modified Time: 437\r\n      Debug: Off\r\n      Object Name:\r\n      Observers:\r\n        none\r\n      Pointer: 000001BC56DA91C0\r\n      Container manages memory: true\r\n      Size: 22500\r\n      Capacity: 22500\r\n\r\n     Moving image = Image (000001BC56DA33F0)\r\n  RTTI typeinfo:   class itk::Image<double,2>\r\n  Reference Count: 2\r\n  Modified Time: 620\r\n  Debug: Off\r\n  Object Name:\r\n  Observers:\r\n    none\r\n  Source: (none)\r\n  Source output name: (none)\r\n  Release Data: Off\r\n  Data Released: False\r\n  Global Release Data: Off\r\n  PipelineMTime: 0\r\n  UpdateMTime: 617\r\n  RealTimeStamp: 0 seconds\r\n  LargestPossibleRegion:\r\n    Dimension: 2\r\n    Index: [0, 0]\r\n    Size: [150, 150]\r\n  BufferedRegion:\r\n    Dimension: 2\r\n    Index: [0, 0]\r\n    Size: [150, 150]\r\n  RequestedRegion:\r\n    Dimension: 2\r\n    Index: [0, 0]\r\n    Size: [150, 150]\r\n  Spacing: [1, 1]\r\n  Origin: [0, 0]\r\n  Direction:\r\n1 0\r\n0 -1\r\n\r\n  IndexToPointMatrix:\r\n1 0\r\n0 -1\r\n\r\n  PointToIndexMatrix:\r\n1 0\r\n0 -1\r\n\r\n  Inverse Direction:\r\n1 0\r\n0 -1\r\n\r\n  PixelContainer:\r\n    ImportImageContainer (000001BC56D78710)\r\n      RTTI typeinfo:   class itk::ImportImageContainer<unsigned long,double>\r\n      Reference Count: 1\r\n      Modified Time: 614\r\n      Debug: Off\r\n      Object Name:\r\n      Observers:\r\n        none\r\n      Pointer: 000001BC56DD9690\r\n      Container manages memory: true\r\n      Size: 22500\r\n      Capacity: 22500\r\n\r\n     Weighting = 0.5\r\n     Sampling strategy = none\r\n     Number of bins = 32\r\n     Radius = 4\r\n     Sampling percentage  = 1\r\n   Transform = TimeVaryingVelocityField\r\n     Gradient step = 2\r\n     Update field sigma (voxel space) = 1\r\n     Total field sigma (voxel space) = 0.05\r\n     Update field time sigma = 0\r\n     Total field time sigma  = 0\r\n     Number of time indices = 8\r\n     Number of time point samples = 8\r\nRegistration using 1 total stages.\r\n\r\nStage 0\r\n  iterations = 1200x1200x100x20x0\r\n  convergence threshold = 0\r\n  convergence window size = 5\r\n  number of levels = 5\r\n  using the Demons metric (weight = 0.5)\r\n  preprocessing:  histogram matching the images\r\n  using the MeanSquares metric (weight = 1)\r\n  preprocessing:  histogram matching the images\r\n  Shrink factors (level 1 out of 5): [8, 8]\r\n  Shrink factors (level 2 out of 5): [6, 6]\r\n  Shrink factors (level 3 out of 5): [4, 4]\r\n  Shrink factors (level 4 out of 5): [2, 2]\r\n  Shrink factors (level 5 out of 5): [1, 1]\r\n  smoothing sigmas per level: [8, 6, 4, 2, 1]\r\n  Using default NONE metricSamplingStrategy\r\n/cygdrive/d/ANTs_2.1.0_Windows/Release/c_example.sh: 行 15:  9268 Segmentation fault      ./antsRegistration -d $dim -m demons[ $f,$m, 0.5, 0 ] -m meansquares[ $f,$m, 1, 0 ] -t TimeVaryingVelocityField[ 2.0, 8, 1,0.0, 0.05,0 ] -c $its -s $smth -f $down -u 1 -o [output/ex_,output/ex_diff.nii.gz,output/ex_diff_inv.nii.gz]\r\n/cygdrive/d/ANTs_2.1.0_Windows/Release/c_example.sh: 行 17:  5624 Segmentation fault      ./ConvertToJpg output/grid.nii.gz figures/grid.png\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/stnava/ANTs/issues/comments/262431449","html_url":"https://github.com/stnava/ANTs/issues/389#issuecomment-262431449","issue_url":"https://api.github.com/repos/stnava/ANTs/issues/389","id":262431449,"user":{"login":"dorianps","id":9083517,"avatar_url":"https://avatars.githubusercontent.com/u/9083517?v=3","gravatar_id":"","url":"https://api.github.com/users/dorianps","html_url":"https://github.com/dorianps","followers_url":"https://api.github.com/users/dorianps/followers","following_url":"https://api.github.com/users/dorianps/following{/other_user}","gists_url":"https://api.github.com/users/dorianps/gists{/gist_id}","starred_url":"https://api.github.com/users/dorianps/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dorianps/subscriptions","organizations_url":"https://api.github.com/users/dorianps/orgs","repos_url":"https://api.github.com/users/dorianps/repos","events_url":"https://api.github.com/users/dorianps/events{/privacy}","received_events_url":"https://api.github.com/users/dorianps/received_events","type":"User","site_admin":false},"created_at":"2016-11-23T04:12:19Z","updated_at":"2016-11-23T04:12:19Z","body":"A side note, you can install ANTs in Windows 10 using Windows Linux\nSubsystem. The benefit is that you can go straight the the latest code and\nget updates immediately. Windows releases of ANTs are not that recent.\n\nInstructions for installing ANTs in WLS are at the end of this page\n<https://github.com/stnava/ANTsR/wiki/Installing-ANTsR-in-Windows-10-(along-with-FSL,-Rstudio,-Freesurfer,-etc).>\n.\n\nDorian\n\nOn Tue, Nov 22, 2016 at 10:52 PM, shansiliu <notifications@github.com>\nwrote:\n\n> Sorry....which two files?\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/stnava/ANTs/issues/389#issuecomment-262429843>, or mute\n> the thread\n> <https://github.com/notifications/unsubscribe-auth/AIqafc0pc_kICvJ-X-EM6rP69HZFGzpKks5rA7hygaJpZM4K6LaQ>\n> .\n>\n"}}
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