Registration process error (no Settings.images)

Forums Forums Surface and Volume Registration (SVReg) Registration process error (no Settings.images)

Viewing 10 reply threads
  • Author
    Posts
    • #293
      ftadel
      Participant

      Hello,
      I got the error while processing the MRI from the Brainstorm tutorial: http://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite
      (btw: this tutorial needs to be updated a bit…)
      Francois


      Welcome to BrainSuite16a (build #2756, built with Qt 5.6.1, compiled with MSVC2013 on Jul 12 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\BrainSuite16a
      Using SVReg installed in directory C:\Program Files\BrainSuite16a\svreg
      Autosave Prefix is D:\RawData\Anatomy\Subjects\PD\brainsuite_16a/pd
      Using Autosave Prefix:D:\RawData\Anatomy\Subjects\PD\brainsuite_16a\pd
      Finished file preparation 0.001
      Executing: C:\Program Files\BrainSuite16a\svreg\bin\svreg_label_surf_hemi.exe D:\RawData\Anatomy\Subjects\PD\brainsuite_16a\pd C:\Program Files\BrainSuite16a\svreg\BrainSuiteAtlas1\mri left -v1
      Executing: C:\Program Files\BrainSuite16a\svreg\bin\svreg_label_surf_hemi.exe D:\RawData\Anatomy\Subjects\PD\brainsuite_16a\pd C:\Program Files\BrainSuite16a\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 = 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\BrainSuite16a\svreg\bin\warp_points.exe
      Registering corpus callosum curve
      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
      No appropriate method, property, or field ‘images’ for class ‘Settings’.

      Error in iptgetpref (line 50)
      Error in useIPPLibrary (line 15)
      Error in imfilter>useIPPL (line 296)
      Error in imfilter>filterPartOrWhole (line 347)
      Error in imfilter (line 179)
      Error in imgaussian (line 36)
      Error in curvature_registration512g_wt_multi_bs_elastic_xyz_cg (line 62)
      Error in curvature_registration_newbs_elastic_xyz (line 73)
      Error in svreg_label_surf_hemi (line 166)
      MATLAB:noSuchMethodOrField

      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
      New 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\BrainSuite16a\svreg\bin\warp_points.exe
      Registering corpus callosum curve
      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
      No appropriate method, property, or field ‘images’ for class ‘Settings’.

      Error in iptgetpref (line 50)
      Error in useIPPLibrary (line 15)
      Error in imfilter>useIPPL (line 296)
      Error in imfilter>filterPartOrWhole (line 347)
      Error in imfilter (line 179)
      Error in imgaussian (line 36)
      Error in curvature_registration512g_wt_multi_bs_elastic_xyz_cg (line 62)
      Error in curvature_registration_newbs_elastic_xyz (line 73)
      Error in svreg_label_surf_hemi (line 166)
      MATLAB:noSuchMethodOrField

      Register and Label Brain took 7:05.278

    • #294
      Anand Joshi
      Moderator

      Hi Francois,
      Thank you for reporting this. Did you get similar errors on other datasets (if you have processed other brains) with BrainSuite or only this one?
      Anand

    • #295
      ftadel
      Participant

      It’s the only one I tried…

      • #296
        Anand Joshi
        Moderator

        Hi Francois,
        BrainSuite+SVReg is running fine on my computer so far. It has passed the stage where it showed error.
        I am working with sample_auditory dataset. I downloaded it from brainstorm site, created a new subject in brainstorm and imported anatomy for sample_auditory there. Then I exported the mri as T1.nii
        I ran brainsuite on this data with default parameters, except at skull extraction, I chose Edge constant=0.63 and Erosion Size=2.
        Can you please make sure that this change was done when you ran the sequence? It could have caused bad extraction and then error later.

        The following was mentioned on the BrainSuite tutorial webpage on the BrainStorm site but now seems to be removed in the subsequent edits. I will reinsert it. Hope that it is fine.

        For this tutorial data, the parameters for skull extraction need to be changed to get optimal results. Please set ‘Edge Constant=0.63’ and ‘Erosion Size=2’.

        Thanks,
        Anand

    • #297
      ftadel
      Participant

      Hi Anand,

      I got exactly the same error with the default values and with Edge Constant=0.63 and Erosion Size=2.
      Except that in the second case (modified values), the pole of the frontal lobes is missing.
      I removed this line from the tutorial because modifying these values was giving results that were worse than with the default values.

      The file that should be processed in this tutorial is the following (I fixed the download link):
      ftp://neuroimage.usc.edu/pub/auditory_tutorial_T1.zip

      Right now I cannot use BrainSuite 16a on Windows 10 because the SVReg step is not working.

      Francois

      • #298
        Anand Joshi
        Moderator

        Hi Francois,
        I tried the volume you shared and it ran fine with all default parameters (no change in skull extraction or other parameters).
        Can you try with default parameters and if it fails, can you please share the directory with all the outputs generated up to that point? I will try to see if I can figure out where things are diverging compared to my run on the same subject.
        Thanks,
        Best,
        Anand

    • #299
      ftadel
      Participant
    • #300
      Anand Joshi
      Moderator

      Hi Francois,
      I am running SVReg sequence on the data that you shared and it is running fine. Do you have full Matlab or MCR for 2015b installed at the default location? Perhaps, one thing to try is that you have Matlab MCR for 2015b installed in default location. If you have any suggestions on how I can reproduce this error, that would be helpful. Do you have anything special in your Matlab/Windows installation (added third party library etc)? Anand

    • #301
      ftadel
      Participant

      I have both the MCR 2015b and MATLAB 2015b installed on my computer.
      None of them are in “standard installation path”.
      I do not have any additional libraries saved in my Matlab path.

      How do you define from BrainSuite what is the base folder of Matlab?

      NB: You should never be relying on “standard path”, this cannot be deployed properly.
      On Windows systems, you can get the installation folders from the following registry keys:
      HKLM\SOFTWARE\MathWorks\MATLAB\9.0
      HKLM\SOFTWARE\MathWorks\MATLAB Runtime\9.0
      HKLM\SOFTWARE\Wow6432Node\MathWorks\MATLAB\9.0
      HKLM\SOFTWARE\Wow6432Node\MathWorks\MATLAB Runtime\9.0
      Check the script brainstorm3/bin/R2015b/brainstorm3.bat for example on how to get these values from a shell script.

      • #302
        Anand Joshi
        Moderator

        Hi Francois,
        Thanks, if you are using windows system, then the compiled exe will figure out the path for MCR or Matlab runtime automatically, based on registry keys I think, but for Linux and Mac, one has to do some modifications to the svreg script.
        I have never seen this error before and cann’t reproduce it here, so not sure how to proceed. I am trying it on another computer. If you have any suggestion on how to reproduce it here it would be helpful. Since the error came from settings of image processing toolbox, did you have any change in setting for that toolbox?
        Anand

    • #303
      ftadel
      Participant

      I don’t have the signal processing toolbox in my MATLAB installation, I guess this is the source of the error.

      In this case, I guess I should specify that I want to use the MCR instead of the full Matlab installation.
      How can I change the Matlab base path that is used in BrainSuite?

    • #304
      Anand Joshi
      Moderator

      According to the following link, it should not matter, but it also says the following.

      http://www.mathworks.com/help/compiler/install-the-matlab-runtime-and-matlab-on-the-same-machine.html

      Windows
      To run deployed MATLAB code against MATLAB Runtime install, mcr_root\ver\runtime\win32|win64 must appear on your system path before matlabroot\runtime\win32|win64.
      If mcr_root\ver\runtime\arch appears first on the compiled application path, the application uses the files in the MATLAB Runtime install area.
      If matlabroot\runtime\arch appears first on the compiled application path, the application uses the files in the MATLAB installation area.

      It is worth trying to set environment PATH variable such that MCR appears before Matlab.

    • #306
      ftadel
      Participant

      I exchanged the order of the two folders (MATLAB and MCR) in the system path and it looks like it’s working!
      Thanks

    • #307
      ftadel
      Participant

      However, the results are better with the default parameters than with ‘Edge Constant=0.63’ and ‘Erosion Size=2’. If we do what you recommend on this MRI, there is a part of the frontal lobes that is not classified as brain and that is not included in the final cortex surfaces.

      Can you please double-check this and then delete the comment you added again on the Brainstorm tutorial?
      Thanks
      Francois

      • #308
        Anand Joshi
        Moderator

        Hi Francois,
        Yes, the default parameters work better for this volume and I deleted the comment about parameter change.
        Thanks,
        Anand

Viewing 10 reply threads
  • You must be logged in to reply to this topic.