MATLAB Tools

• PLS program
  
  Partial least squares (PLS), which was first introduced to the neuroimaging community in 1996, has proven to be a robust method for extracting distributed signal changes related to changing task demands.
• Tools for NIfTI and ANALYZE image in MATLAB
  
  These tools can help you to handle both ANALIZE and NIfTI file formats.

  • If you are confused by the Left side / Right side of an ANALYZE image, the following link may help you:
    http://www.rotman-baycrest.on.ca/~jimmy/UseANALYZE.htm
  • Feature of load_untouch_header_only:  It will load exactly whatever stored in the header section of NIfTI or ANALYZE data, and automatically detected the input file format. NIfTI structure will be returned for NIfTI file, and ANALYZE structure will be returned for ANALYZE file.
  • Feature of load_nii:  It not only loads the file, but also transforms the affine matrix to a diagonal matrix with positive entries and re-orients the image matrix in the loaded structure correspondingly. This feature makes it different from other software, and it is proven to be a convenient way to tell the orientation immediately, especially in the Left / Right confusion. For NIfTI data with both non-zero sform_code & qform_code, load_nii even allows you to pick your preferred form, also sform_code is picked by default.
  • Feature of view_nii:  It can display & edit the background image, as well as the overlay activation map and ROI etc. If you use this function in your application, the display can be embedded into your existing figure window. If you use it as an individual program, it can also edit the orientation and voxel value of the image, and save the modified image. See detail at:
    http://www.rotman-baycrest.on.ca/~jimmy/NIfTI/examples.txt
  • Feature of reslice_nii:  It can interpolate any oblique images with non-orthogonal rotation or shearing and save them into orthogonal orientations that can be loaded with load_nii.
  • Feature of save_nii:  It can save any NIfTI data into ANALIZE compatible file extension (.img/.hdr), and can be used by other software that does not support NIfTI file format.
• Affine Transformation
  
  This program can handle both 2D and 3D affine transformation. It uses affine matrix to rotate, translate, scale, reflect and shear a 2D image or 3D volume.
• 3D Bresenham's line generation
  
  This program can produces the X Y Z coordinates of a 3D Bresenham's line between two given points. If set Z=0, it produces a 2D Bresenham's line.
• Load BIOPAC ACQ (AcqKnowledge file) format data
  
  This program can load BIOPAC's AcqKnowledge (ACQ) data to a structure containing ACQ header field and data matrix field. It is based on Application Note 156 on their web site, which supports up to ACQ 3.9. It can also read ACQ 4.0 & 4.1 data based on Nathan Vack's open source code.
• Edit plotted data with mouse
  
  This program can edit plotted data by picking any point on the curve and moving the mouse. It demonstrated how to write GUI and handle mouse movement in old MATLAB versions.
• geotiffwrite
  
  This program can write a 2D or 3D array to a single or multi-band GeoTIFF file, with a GUI window to select GeoTIFF parameters.