registration process error

Forums Forums Surface and Volume Registration (SVReg) registration process error

This topic contains 22 replies, has 6 voices, and was last updated by  Anand Joshi 5 months, 2 weeks ago.

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  • #376

    yunliaoyu
    Participant

    Hello:
    I encountered an error during register and label brain process.It seems like .warp file cannot be read.I have tried many ways but still cannot fix it. Would you please help me to know what is wrong? Thanks! BTW, I use windows and I am sure that MATLAB MCR is installed.

    Following is the detailed Brainsuite log:
    Welcome to BrainSuite16a1 (build #2777, built with Qt 5.6.1, compiled with MSVC2013 on Sep 15 2016)
    Copyright (C) 2016 The Regents of the University of California
    This program is free software and is released under a GNU General Public License; Version 2. For more details, please see the enclosed license files.
    BrainSuite uses the Qt GUI Toolkit. The Qt GUI Toolkit is Copyright (C) 2015 Digia Plc and/or its subsidiary(-ies) and is licensed under the LGPL v2.1.
    BrainSuite install directory: C:\Program Files\BrainSuite16a1
    Using SVReg installed in directory C:\Program Files\BrainSuite16a1\svreg
    Autosave Prefix is F:\wangxu\mri_bs_test/T1.bfc
    Using Autosave Prefix:F:\wangxu\mri_bs_test\T1.bfc
    Finished file preparation 0.000
    Executing: C:\Program Files\BrainSuite16a1\svreg\bin\svreg_label_surf_hemi.exe F:\wangxu\mri_bs_test\T1.bfc C:\Program Files\BrainSuite16a1\svreg\BrainSuiteAtlas1\mri left -v1
    Executing: C:\Program Files\BrainSuite16a1\svreg\bin\svreg_label_surf_hemi.exe F:\wangxu\mri_bs_test\T1.bfc C:\Program Files\BrainSuite16a1\svreg\BrainSuiteAtlas1\mri right -v1
    Error running surface labeling. Processing halted.
    left log:
    —–
    Labeling left hemisphere
    Computing mid cortical surfaces
    Checking Euler Characteristic of input surfaces, it should be 1
    Euler characteristic of left Hemi = 9
    New Euler characteristic of left Hemi = -2
    Computing Smooth cortical representation
    Generating Smooth representations of the surface
    Performing L2 registration and flattening
    Computing faces and vertices connectivity
    Applying deformation field from AIR
    Pausing for 5 sec. to clear file buffers
    Using Executable C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe
    SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
    Error using readdfs (line 61)
    Unable to read:F:\wangxu\mri_bs_test\T1.bfc.svreg.tmp\T1.bfc.target.left.mid.cortex_smooth10_smooth10.dfs

    Error in surf_align_autocorrect_with_AIR (line 159)

    Error in align_surf_curves (line 62)

    Error in surf_flatten_newbs (line 32)

    Error in svreg_label_surf_hemi (line 164)

    right log:
    —–
    Labeling right hemisphere
    Computing mid cortical surfaces
    Checking Euler Characteristic of input surfaces, it should be 1
    Euler characteristic of right Hemi = -10
    New Euler characteristic of right Hemi = -12
    Computing Smooth cortical representation
    Generating Smooth representations of the surface
    Performing L2 registration and flattening
    Computing faces and vertices connectivity
    Applying deformation field from AIR
    Pausing for 5 sec. to clear file buffers
    Using Executable C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe
    SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
    Error using readdfs (line 61)
    Unable to read:F:\wangxu\mri_bs_test\T1.bfc.svreg.tmp\T1.bfc.right.mid.cortex_smooth10_smooth10.dfs

    Error in surf_align_autocorrect_with_AIR (line 160)

    Error in align_surf_curves (line 62)

    Error in surf_flatten_newbs (line 32)

    Error in svreg_label_surf_hemi (line 164)

    Register and Label Brain took 1:08.308

    It will help a lot if you reply.Thanks!

    XU WANG

  • #377

    Anand Joshi
    Moderator

    Is there a file F:\wangxu\mri_bs_test\T1.bfc.warp ?

    • #378

      yunliaoyu
      Participant

      yes´╝îI have that file.

  • #379

    Anand Joshi
    Moderator

    Hi Xu, Is your data on external hard drive? If yes then can you please try copying it on internal drive and then running the program? The speed of the external drive may not be enough for data processing. Please let me know.

    • #380

      yunliaoyu
      Participant

      Hi,The data I processed is on the internal drive. I checked the log again and found that I only have F:\wangxu\mri_bs_test\T1.bfc.svreg.tmp\T1.bfc.target.left.mid.cortex_smooth10.dfs. But the file that mentioned in the log is F:\wangxu\mri_bs_test\T1.bfc.svreg.tmp\T1.bfc.target.left.mid.cortex_smooth10_smooth10.dfs. Is it the problem? Looking forward to your reply! Thanks!

  • #381

    Anand Joshi
    Moderator

    Can you try running the surface extraction sequence again? My guess is that for some reason .warp file is corrupted leading to the error in later stages. If it is possible for you to share the data with me, I can try running it.

    • #382

      yunliaoyu
      Participant

      I have tried running the extract sequence again and using another file, but still encountered this error. Of course I can share my data with you. It is of great help if you run it. Would you please tell me your email? Thanks!

  • #386

    Anand Joshi
    Moderator

    My email ID is ajoshi@sipi.usc.edu. You are using 64 bit windows platform, right?

    • #387

      yunliaoyu
      Participant

      Yes, I used 64 bit windows platform. I sent a file I used in this process to you by E-mail. Thanks for your help!

  • #457

    Anand Joshi
    Moderator

    I am not able to find your email. What was the subject or email address from which you sent it?

  • #473

    yunliaoyu
    Participant

    maybe some error occurred in my mail system. I resent you a E-mail. The subject is ‘nii file for running cortical surface extraction sequence’ and my E-mail address is wangxu2011@sjtu.edu.cn

  • #553

    tenamber
    Participant

    Hey, I experience the exact same Problem.
    Has this been solved somehow?
    Thanks, Frederik

  • #554

    Anand Joshi
    Moderator

    Hi, Thank you for reporting the issue.
    Are you able to run the following exe from the command line
    > C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe

    It should show the following message.
    > C:\Users\ajoshi>”C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe”
    >
    > Usage: C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe .warp_file ucf_in ucf_out

    Please let me know what message you get.
    Additionally, please make sure that your windows system is up to date with all the updates applied.
    Can you please report your windows system configuration?
    Thanks,
    Anand

    • This reply was modified 1 year, 11 months ago by  Anand Joshi. Reason: updates
    • This reply was modified 1 year, 11 months ago by  Anand Joshi.
  • #557

    Anand Joshi
    Moderator

    A possible fix it installing 32 bit redistributable from:
    https://www.microsoft.com/en-us/download/details.aspx?id=40784
    Make sure to install 32bit version of Visual C++ Redistributable Packages for Visual Studio 2013.

  • #648

    gee306
    Participant

    After installed the 32bit version of Visual C++ Redistributable Packages

    I have already solve the same problem.

    It has bothered me a long time.

    Thanks Anand Joshi !

  • #1116

    abhinavdhere
    Participant

    Dear Prof. Joshi,
    Both the BrainSuite software and SVreg are useful tools. However, I am facing the exactly same issue as faced by yunliaoyu, but for 64 bit Linux (Ubuntu 16.04) and BrainSuite 17a. Naturally the Visual Studio fix doesn’t seem useful in this case.
    Kindly suggest if there is a fix available for Linux also?
    Thanks.

  • #1117

    Anand Joshi
    Moderator

    Can you please type the error log here?

  • #1118

    abhinavdhere
    Participant

    Thanks for quick response. The log is as follows:

    left log:
    —–
    Labeling left hemisphere
    Computing mid cortical surfaces
    Checking Euler Characteristic of input surfaces, it should be 1
    Euler characteristic of left Hemi = 1
    Computing Smooth cortical representation
    Generating Smooth representations of the surface
    Performing L2 registration and flattening
    Computing faces and vertices connectivity
    Applying deformation field from AIR
    Pausing for 5 sec. to clear file buffers
    ans =
    1
    Using Executable /home/abhinav/BrainSuite17a/svreg/bin/warp_points_linux
    As non-owner and non-group member, you lack write permission for the specified file or directory. (AIR_WORLD_CANT_WRITE_ERROR)
    As non-owner and non-group member, you lack write permission for the specified file or directory. (AIR_WORLD_CANT_WRITE_ERROR)
    Registering corpus callosum curve
    ans =
    1
    The register_cc_curve program as a part of the RCC package is provided under the terms
    of the GNU General Public License, version 2 as published by
    the Free Software Foundation.
    RCC is based on Coherent Point Drift (CPD) Package provided from
    https://sites.google.com/site/myronenko/research/cpd
    RCC package is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
    GNU General Public License for more details.
    You should have received a copy of the GNU General Public License
    along with RCC package; if not, write to the Free Software
    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
    Performing L2 registration
    L2 distance minimization started. This can take 10-15 min.
    L2 distance minimization is done
    Mapping to unit square
    Performing curvature registration
    Calculating Multiresolution curvature maps
    Multiresolution curvature maps are calculated
    Computing additive curvature
    Performing curvature registration

    The Laplacian matrix takes 23035912 bytes

    linesearch step too small
    iter 1/50 f = 50.7582, linesearch iter=39
    iter 2/50 f = 295.532, linesearch iter=4
    iter 3/50 f = 289.286, linesearch iter=10
    iter 4/50 f = 286.968, linesearch iter=6
    iter 5/50 f = 278.225, linesearch iter=9
    iter 6/50 f = 276.886, linesearch iter=11
    iter 7/50 f = 276.864, linesearch iter=12
    iter 8/50 f = 276.647, linesearch iter=13
    iter 9/50 f = 276.647, linesearch iter=13
    iter 10/50 f = 276.647, linesearch iter=14
    iter 11/50 f = 276.647, linesearch iter=17
    iter 12/50 f = 276.647, linesearch iter=17
    iter 13/50 f = 276.647, linesearch iter=17
    iter 14/50 f = 276.647, linesearch iter=19
    Negative Jacobians in surf reg step = 0/262144

    The Laplacian matrix takes 23035912 bytes

    linesearch step too small
    iter 1/50 f = 170.919, linesearch iter=37
    iter 2/50 f = 322.2, linesearch iter=4
    iter 3/50 f = 313.142, linesearch iter=9
    iter 4/50 f = 305.543, linesearch iter=7
    iter 5/50 f = 300.156, linesearch iter=8
    iter 6/50 f = 299.671, linesearch iter=10
    iter 7/50 f = 299.671, linesearch iter=13
    iter 8/50 f = 299.671, linesearch iter=13
    iter 9/50 f = 299.671, linesearch iter=15
    iter 10/50 f = 299.671, linesearch iter=16
    iter 11/50 f = 299.671, linesearch iter=17
    Negative Jacobians in surf reg step = 0/262144

    The Laplacian matrix takes 23035912 bytes

    linesearch step too small
    iter 1/50 f = 275.207, linesearch iter=36
    iter 2/50 f = 429.659, linesearch iter=3
    iter 3/50 f = 402.783, linesearch iter=12
    iter 4/50 f = 400.133, linesearch iter=8
    iter 5/50 f = 399.817, linesearch iter=10
    iter 6/50 f = 399.792, linesearch iter=10
    iter 7/50 f = 399.767, linesearch iter=12
    iter 8/50 f = 399.764, linesearch iter=12
    iter 9/50 f = 399.762, linesearch iter=13
    iter 10/50 f = 399.761, linesearch iter=13
    iter 11/50 f = 399.761, linesearch iter=14
    iter 12/50 f = 399.76, linesearch iter=14
    iter 13/50 f = 399.76, linesearch iter=14
    iter 14/50 f = 399.76, linesearch iter=15
    iter 15/50 f = 399.76, linesearch iter=18
    iter 16/50 f = 399.76, linesearch iter=18
    iter 17/50 f = 399.76, linesearch iter=19
    iter 18/50 f = 399.76, linesearch iter=19
    Negative Jacobians in surf reg step = 0/262144

    The Laplacian matrix takes 23035912 bytes

    linesearch step too small
    iter 1/50 f = 386.463, linesearch iter=35
    iter 2/50 f = 526.192, linesearch iter=3
    iter 3/50 f = 488.092, linesearch iter=14
    iter 4/50 f = 487.941, linesearch iter=11
    iter 5/50 f = 487.93, linesearch iter=12
    iter 6/50 f = 487.926, linesearch iter=14
    iter 7/50 f = 487.926, linesearch iter=15
    iter 8/50 f = 487.926, linesearch iter=16
    iter 9/50 f = 487.926, linesearch iter=18
    iter 10/50 f = 487.926, linesearch iter=18
    iter 11/50 f = 487.926, linesearch iter=18
    Negative Jacobians in surf reg step = 0/262144
    Curvature registration done.
    Transferring Labels
    left hemisphere done
    Transferring Curves
    Labeling of a hemisphere is done!

    right log:
    —–
    Labeling right hemisphere
    Computing mid cortical surfaces
    Checking Euler Characteristic of input surfaces, it should be 1
    Euler characteristic of right Hemi = 1
    Computing Smooth cortical representation
    Generating Smooth representations of the surface
    Performing L2 registration and flattening
    Computing faces and vertices connectivity
    Applying deformation field from AIR
    Pausing for 5 sec. to clear file buffers
    ans =
    1
    Using Executable /home/abhinav/BrainSuite17a/svreg/bin/warp_points_linux
    As non-owner and non-group member, you lack write permission for the specified file or directory. (AIR_WORLD_CANT_WRITE_ERROR)
    As non-owner and non-group member, you lack write permission for the specified file or directory. (AIR_WORLD_CANT_WRITE_ERROR)
    SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
    Error using readdfs (line 61)
    Unable to read:/home/abhinav/somePath/CAHI01M.svreg.tmp/CAHI01M.target.right.mid.cortex_smooth10_smooth10.dfs
    Error in surf_align_autocorrect_with_AIR (line 159)
    Error in align_surf_curves (line 62)
    Error in surf_flatten_newbs (line 32)
    Error in svreg_label_surf_hemi (line 163)

    Pls. note that this is despite the fact that I have run the program as sudo and have ensured that mri.warp is allowed to execute as program and access is read only to others, read and write to user.

  • #1131

    abhinavdhere
    Participant

    Thanks a lot for your time. I resolved that issue myself.
    It seems the problem was that I was trying to do the SVreg process directly on pial surface, without hemisphere labeling. Performing hemisphere labeling step before registration resolved the issue.

    Now I have the labeled surface with the 95 ROIs color coded. However, I’m not sure how to visualize any sulcal markings (the atlas description has 26 sulci). My primary motive here was to obtain automatic marking of those 26 sulci on the surface.

  • #1178

    Anand Joshi
    Moderator

    You can drag and drop dfc files in brainsuite interface to see the sulci.

  • #1199

    Renatar
    Participant

    Hi, I have the same issue. Something is wrong with the warp_points.exe file. The program just stops to work with “Registration error” message. The log is:

    Welcome to BrainSuite18a (build #3115, built with Qt 5.6.3, compiled with MSVC2015 on Feb 28 2018)
    Copyright (C) 2018 The Regents of the University of California
    This program is free software and is released under a GNU General Public License; Version 2. For more details, please see the enclosed license files.
    BrainSuite uses the Qt GUI Toolkit. The Qt GUI Toolkit is Copyright (C) 2015 Digia Plc and/or its subsidiary(-ies) and is licensed under the LGPL v2.1.
    BrainSuite install directory: C:\Program Files\BrainSuite18a
    Using SVReg installed in directory C:\Program Files\BrainSuite18a\svreg
    Finished file preparation 0.000
    Executing: C:\Program Files\BrainSuite18a\svreg\bin\svreg_label_surf_hemi.exe D:\ADMI\BrainSuite\tests\d\IXI603-HH-2701-T1 C:\Program Files\BrainSuite18a\svreg\BrainSuiteAtlas1\mri left -v1
    Executing: C:\Program Files\BrainSuite18a\svreg\bin\svreg_label_surf_hemi.exe D:\ADMI\BrainSuite\tests\d\IXI603-HH-2701-T1 C:\Program Files\BrainSuite18a\svreg\BrainSuiteAtlas1\mri right -v1
    Error running surface labeling. Processing halted.
    left log:
    —–
    Labeling left hemisphere
    Computing mid cortical surfaces
    Checking Euler Characteristic of input surfaces, it should be 1
    Euler characteristic of left Hemi = -3
    New Euler characteristic of left Hemi = -3
    Computing Smooth cortical representation
    Generating Smooth representations of the surface
    Performing L2 registration and flattening
    Computing faces and vertices connectivity
    Applying deformation field from AIR
    Pausing for 5 sec. to clear file buffers
    Using Executable C:\Program Files\BrainSuite18a\svreg\bin\warp_points.exe
    SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
    Error using readdfs (line 61)
    Unable to read:D:\ADMI\BrainSuite\tests\d\IXI603-HH-2701-T1.svreg.tmp\IXI603-HH-2701-T1.target.left.mid.cortex_smooth10_smooth10.dfs

    Error in surf_align_autocorrect_with_AIR (line 159)

    Error in align_surf_curves (line 62)

    Error in surf_flatten_newbs (line 32)

    Error in svreg_label_surf_hemi (line 163)

    right log:
    —–
    Labeling right hemisphere
    Computing mid cortical surfaces
    Checking Euler Characteristic of input surfaces, it should be 1
    Euler characteristic of right Hemi = 1
    Computing Smooth cortical representation
    Generating Smooth representations of the surface
    Performing L2 registration and flattening
    Computing faces and vertices connectivity
    Applying deformation field from AIR
    Pausing for 5 sec. to clear file buffers
    Using Executable C:\Program Files\BrainSuite18a\svreg\bin\warp_points.exe
    SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
    Error using readdfs (line 61)
    Unable to read:D:\ADMI\BrainSuite\tests\d\IXI603-HH-2701-T1.svreg.tmp\IXI603-HH-2701-T1.target.right.mid.cortex_smooth10_smooth10.dfs

    Error in surf_align_autocorrect_with_AIR (line 159)

    Error in align_surf_curves (line 62)

    Error in surf_flatten_newbs (line 32)

    Error in svreg_label_surf_hemi (line 163)

  • #1200

    Anand Joshi
    Moderator

    Is your windows system 32 bit o 64 bit?
    Is the pial surface generated correctly?

  • #1207

    Anand Joshi
    Moderator

    Please try installing
    Visual C++ Redistributable Packages for Visual Studio 2013

    available from
    https://www.microsoft.com/en-us/download/details.aspx?id=40784

    Make sure to get

    vcredist_x64.exe

    After this the programs should work.

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