These values can be obtained from an SPM Results output at the bottom right of the Graphics window labeled “Smootheness FWHM = X.X Y.Y Z.Z (mm)”. Though we often smooth our functional images with a 6mm FWHM (full-width half-maximum) Gaussian filter, the images have inherent smoothness that is slightly larger. # –fwhmx 8.5 –fwhmy 8.9 –fwhmz 8.3 – Specifies the smoothness in the x, y and z-direction of the image. AlphaSim will determine how many contiguous voxels within your search volume must exceed this statistical threshold to meet correction criteria. More than or fewer than 1000 simulations can be run but 1000 should be sufficient to be confident in the results. This parameter specifies how many simulations to run. # –iter 1000 – AlphaSim works by computing random values and determining cluster extents that meet a statistical threshold. The image file describes the size and contour of the search volume. This file is typically a mask image (voxel values = 0 or 1). AlphaSim will read image resolution and # of voxels in mask from this file. Alternatively, a space can be defined (see AlphaSim manual). # –mask /path/for/maskfile.hdr – Specifies the use of a mask file. # /usr/local/bin/afni/AlphaSim – Specifies the location of the AlphaSim program 05 –fwhmx 8.5 –fwhmy 8.9 –fwhmz 8.3 –rmm 2.1 –out /path/for/outputfile.txt usr/local/bin/afni/AlphaSim –mask /path/for/maskfile.hdr –iter 1000 –pthr. A more complete documentation of associated parameters is contained in the AlphaSim.pdf manual by Douglas Ward.Īn example run of AlphaSim can be executed by typing the following into the command window: The most commonly used approach for AlphaSim is detailed below. Alternative methods include family-wise error (FWE) and false-discovery rate (FDR) correction. A similar statistical and cluster threshold method is described in Forman et al., (1995) Magn Reson Med 33(5):636-47. (Repeat) AlphaSim is a software program that can be used to empirically derive a combination statistical and cluster threshold that effectively corrects for multiple comparisons.

Type AlphaSim to see a summary of how to input arguments.

type “qinteract” to mount the design node, and enter your password.

Luckily, AFNI is already installed on the cluster, (as it works best with Linux and they prefer that you do not install it on Windows.) Installing all of AFNI is required to get AlphaSim up and running.

AlphaSim is a software program that can be used to empirically derive a combination statistical and cluster threshold that effectively corrects for multiple comparisons. AlphaSim is a program included in AFNI (). We have documentation for AFNI because of AlphaSim.

Alphasim spitfire