vcylarim

vcylarim is the core tool of the Cylarim package. It expects as input an activation map, a rim image and a metric image. They can be generated using the cylarim-programs called vrim and vmetric. Optionally, they can also be obtained using the software package LayNii. Note that the rim image must use the following codes: 1:(CSF/GM boundary), 2:(WM/GM boundary), 3:(cortex interior).

The output of vcylarim is a file that contains seven images. The first three images contain the GLM-coefficients estimated for the deep, middle and superficial layers. The fourth image contains the intercept values. The following three images contain z-values of the laminar contrasts (deep-middle), (deep-superficial), (middle-superficial). The output of vcylarim is subsequently used by vcylarim_stats to compute various laminar statistics.

The GLM coefficients are estimated separately for each cylinder. In most voxels, several cylinders overlap. In these voxels, the GLM coefficients and results of t-tests between slabs are averaged.

Example:

vcylarim -in zmap.v -out cylstats.v -rim rim.v -metric metric.v -mask mask.v -type glm -nperm 1000 -radius 3

Here, the input is an activation map (zmap.v), a rim image (rim.v), a metric image (metric.v) and a mask image (mask.v). The mask is optional. If present, it will restrict computations to some part of the input image. This may help to reduce computation time. It should be a binary image. The program vcylarim_getmask can help to obtain useful masks. The parameter “-radius” specifies the radii of the cylinders in mm. The parameter “-equivol” specifies whether or not equivolume correction should be applied to each cylinder.

The type of model to be used can be specified by the parameter “-type”. If set to “glm”, a GLM is applied. Alternatively, this parameter can be set to “-type slabs”. In this case, no GLM is fitted. Instead a simple averaging within three slabs (deep,middle,superficial) is done. This is easier and computationally less involved.

The parameter “-nperm 1000” specifies that permutation tests with 1000 permutations are done. These tests compare the three layers (deep,middle, superficial) against each other. During the permutations, a null distribution is estimated by randomly permuting the cortical depth values. If “-nperm” is set to zero, then no permutations are done, and a crude approximations are returned.

vcylarim implements parallel computations uses openmp. The number of processors to use can be specified with the parameter “-j”. The output (cylbeta.v) contains several images as explained above. This file can be analyzed in subsequent processing steps using cylarim_stats.

Parameters of ‘vcylarim’

-help     Prints usage information.
-in       Input file.
-out      Output file.
-mask     Region of interest mask (Optional)
-metric   Metric image (required)
-rim      Rim image (required)
-radius   Cylinder radius in mm. Default: 2
-equivol  Whether to apply equivolume correction [ true | false ]. Default: false
-nperm    Number of permutations. Default: 1000
-type     Type of model [ glm | slabs ]. Default: glm
-j        Number of processors to use, '0' to use all. Default: 0