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Downloading PALM

To obtain the latest version, please visit the repository on GitHub.

PALM can run as a standalone command (i.e., executed directly from the command line/terminal), or inside Octave or Matlab. In Linux and in Mac systems, it can be executed in any of these ways. In Windows, it can be executed inside Matlab or Octave.

Running as a standalone command

It may be much simpler to run PALM as a command directly from the shell in Linux or in Mac, and it can easily be called from scripts. To do so:

  1. Uncompress the downloaded file.
  2. Open the file palm (not to be confused with palm.m). This is a script, inside which you can set whether the script should use Octave or Matlab. If the one that is chosen isn't in the $PATH variable, make sure to specify also the path to the directory that contains the executable for either of these (whichever you choose).
  3. To invoke PALM, simply type ./palm in the directory where it was installed. The path can also be added to the system's $PATH variable, so that it can be easily called from any directory just by typing palm.

If you are using Mac, and choose Octave, note that reading of NIFTI files need the option -noniiclass to work properly (more details below).

Running inside Matlab

Uncompress the downloaded file, open Matlab, and add the newly created directory to the Matlab path (menu File --> Set Path). Typing palm at the prompt without arguments shows usage information. This works for Linux, Mac and Windows.

Running inside Octave

Uncompress the downloaded file, start Octave, and add the newly created directory to the Octave path. This can be done with the command addpath:

addpath('/full/path/to/palm')

This line can be added to the ~/.octaverc file, so that the change becomes permanent (if the ~/.octaverc doesn't exist, an empty file can be created, then the line added). Typing palm at the prompt without arguments shows usage information. This works for Linux and Mac. It can work also with Windows if the paths are entered using the Windows filesystem convention (e.g., C:\example).

For Octave for Mac, note that reading of NIFTI files need the option -noniiclass to work properly (more details below).

For spatial statistics (cluster extent, cluster mass, and TFCE), the Octave package image is required.