BrainSuite

ftadel

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  • August 18, 2016 at 9:47 am in reply to: Registration process error (no Settings.images) #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

      August 18, 2016 at 9:16 am in reply to: Registration process error (no Settings.images) #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

        August 17, 2016 at 4:39 pm in reply to: Registration process error (no Settings.images) #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?

          August 17, 2016 at 2:41 pm in reply to: Registration process error (no Settings.images) #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.

            August 17, 2016 at 12:26 pm in reply to: Registration process error (no Settings.images) #299
            ftadel
            Participant

              Here it is:
              https://www.dropbox.com/s/0ugqmxlptjmqj3g/brainsuite_16a.zip?dl=0

              August 17, 2016 at 7:13 am in reply to: Registration process error (no Settings.images) #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

                August 16, 2016 at 1:20 pm in reply to: Registration process error (no Settings.images) #295
                ftadel
                Participant

                  It’s the only one I tried…

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