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 six images. The first three images contain the coefficients estimated for the deep, middle and superficial layers. 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 layer coefficients are estimated separately for each cylinder. In most voxels, several cylinders overlap. In these voxels, the coefficients are averaged.

Example:

vcylarim -in zmap.v -out cylstats.v -rim rim.v -metric metric.v -mask mask.v -equivol true -type median -nperm 1000 -radius 2

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 crude approximations are returned.

vcylarim implements parallel computations using 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 [ median | | mean | glm ]. Default: median
-j        Number of processors to use, '0' to use all. Default: 0