Skip to Content
MRIcroGL

Troubleshooting

Introduction

If you experience probelms with MRIcroGL, start the program while depressing the SHIFT key (or Control if you are using Linux). You will be asked if you want to reset the program to the default settings – press ‘Yes’. This restores the generic settings for the program.

Old or inexpensive graphics cards

By default, MRIcroGL attempts to show the images in their native resolution. However, this strategy may not work well in two situations: with older video cards the rendering may be very slow, whereas with video cards with little texture memory the images may appear scrambled. To combat either effect, launch MRIcroGL with while holding the shift key down (or control key if you are using Linux). A dialog will appear asking you if you wish to restore the default settings – press “Yes”. Next, a dialog appears ‘Set graphics card (0 = old, 1 = poor, 2 = OK, 3 = great’, providing you with four options:

  1. Enter ‘0’ if you have an old video card (e.g. iMac or MacBook from 2006 or earlier). In this case, the images will be padded to the nearest power-of-two (e.g. an image with a dimension of 217 voxels will be converted to have 256 voxels). Images should still appear ‘Normal’. This selection improves rendering speed on old hardware, but slows rendering speed on modern hardware. To test rendering speed, choose the ‘About MRIcroGL’ menu item – the loaded image will be rotated 360-degrees and the frames per second reported. Therefore, you can test the speed with and without data padding.
  2. Enter ‘1’ for reduced resolution. This will reduce the maximum dimension of any image to 88 voxels. The software should work, but image quality will suffer (see ‘Shrunk’ image). This is required for OSX computers with Intel graphics cards running OSX versions after 10.6.6 and before 10.8.
  3. Enter ‘2’ for standard resolution (256 voxels in each dimension). This should work with most graphics cards (including Sandy Bridge or later Intel Graphics cards). The maximum resolution is set to 256 voxels in each dimension. Images should appear ‘Normal’, but if they appear ‘Scrambled’ restart the software with the shift key down and select a smaller number.
  4. Enter ‘3’ for great resolution (2048 voxels in each dimension). This provides the best performance for modern video cards with adequate texture memory. Images should appear ‘Normal’, but if they appear ‘Scrambled’ restart the software with the shift key down and select a smaller number.
    Finally, a dialog appears ‘Set gradient calculation (0=slow[CPU], 1=fast[GPU])’, providing you with two options: 
    • Enter ‘0’ to use the central processing unit to estimate gradients. This will tend to lead to slow loading of images. Use this only if the fast option causes your computer to crash when loading images. You will want to set this option if you see the error message “Access violation at address 00000000” when the application launches (NVidia video cards from 2009 or earlier running 32-bit Windows XP).
    • Enter ‘1’ to use the graphics card to estimate gradients. For most computers this is the preferred option. The only reason not to use this is if you have a very old graphics card with very little memory for graphics.

Virtualized Environments 

MRIcroGL can run on some virtualized systems using the right versions of VirtualBox (including with 'Enable 3D acceleration'), Mesa (Mesa (7.6 (released in 2009) or later, check using glxinfo) and VirtualGL (vglrun). MacOS and Linux users can type 'glxinfo' at the command line for details about your OpenGL support: glxinfo should report "OpenGL version string: 2.1" (or later). Further, the glxinfo Visuals Table should report Red (r), Green (g), blue (b) of at least 8-bits each and a depth (dpth) of at least 24 bits. Linux users who do not meet these requirements will may see the error message 'gdk_gl_context_share_new_usefpglx context creation failed' when they attempt to run MRIcroGL. You can remedy this by upgrading your graphics driver or hardware.

If your virtualized environment uses X11, be aware that X11's indirect rendering mode is limited to OpenGL 1.4 and earlier. Since MRIcroGL requires OpenGL 2.1, you will need to use direct rendering. SCM provides a terrific page describing the options for running modern OpenGL on remote machines.

 

Advanced Notes 

  • MacBooks, MacBook Airs and Mac Minis that use the Intel HD 3000 Graphics will work correctly in standard mode with OSX 10.6.6 and earlier or 10.8 and later. However, the drivers for intermediate versions of OSX (10.6.7-10.7) require reduced resolution. I remain puzzled why the volumes are limited to around 88^3 (just ~2.6Mb for a RGBA texture).
  • You can also manually adjust these values by editing your MRIcroGL.ini file with a text editor. For Windows, this is stored in the same folder as the executable, for OSX/Linux it is in the hidden folder ~/.mricrogl.
    • ForcePowerOfTwo=0 : Determines whether image is padded to a power of two (1) or not (0). Default is 0.                                      Caltech Mouse Atlas
    • MaxVox=2048 : Sets the maximum resolution loaded: default is 2048, reduced resolution is 88. Note that this is typically used with ForcePowerOfTwo=0, if you set ForcePowerOfTwo=1, then it is strongly suggested you set MaxVol to a power of two (64, 128, 256…).
    • RayCastQuality1to10=4 : Determines sampling rate of each ray. A value of 1 leads to very coarse surfaces (but quick rendering), while a value of 10 leads to precise surfaces (but slow rendering). The value of 4 is the default, but this is adjusted to 8 with reduced resolution (i.e. with a MaxVox of 88, the volumes are very small, so there is little penalty for a fine sampling rate).
  • Power users can can also use the “MaxVox” setting to tune MRIcroGL’s performance for their video card. For example, consider the MNI152_T1_0.5mm image that is distributed with FSL: it has ~5 times more voxels than the ch256 image that ships with MRIcroGL. This huge image may render acceptably on a high end video card, but be very sluggish on a laptop video card. In this case, one might consider setting the laptop for “MaxVox=256”: subsequently the really large MNI152_T1_0.5mm image with 364*436*364 voxels will be interpolated to 214*256*214, and will render with similar speed as the ch256 image. In this case, images with resolutions <=256 voxels will not be influenced, and while the loading of images above this resolution will be slow (as the image is resliced) the subsequent performance will be fast.
  • Debian-based (e.g. Ubuntu) Linux users may see the followng message in the terminal command line 'Gtk-Message: 11:29:20.110: Failed to load module "canberra-gtk-module"'. Feel free to ignore this message. However, if you want you can 'run sudo apt install libcanberra-gtk-m'. This library enables auditory effects for using the graphical interface, e.g. so you can hear a 'click' sound when a button is depressed. It is completely optional. 
  • Linux users where glxinfo reveals they are using Mesa may find that they can use the launch the software from the command line with an override, e.g. MESA_GL_VERSION_OVERRIDE=3.3 MRIcroGL
     
© 2012 University of South Carolina Board of TrusteesPrivacy Policy