vcylarim_plot

The inputs into the program vcylarim_plot are a file containing the GLM-coefficients computed by vcylarim, and also a region of interest (ROI). The original spatial resolution (prior to upsampling) should also be provided. The program produces a txt file as output that can be used for plotting laminar-specific results.

The output txt file contains three rows, one for each layer.

The first row begins with an index ‘0’, and shows results for the deep layer.

The second row begins with an index ‘1’, and shows results for the middle layer.

The second row begins with an index ‘2’, and shows results for the superficial layer.

The second column in each row is the mean value of all beta values within the given ROI of that cortical layer. The third and fourth columns are the lower and upper bounds of the 95 percent confidence interval. The degrees of freedom required for this purpose are approximated by estimating the number of non-zero voxels in the ROI (prior to upsampling), divided by 4, which is generally a very conservative estimate.

Example:

vcylarim_plot -in cylbeta.v -roi roi.nii -resolution 0.8 0.8 0.8 -out list.txt

Example output:

layer ID	mean	lower bound	upper bound
0	0.072	0.052	0.081
1	0.104	0.086	0.125
2	0.048	0.032	0.059

Parameters of ‘vcylarim_plot’

-help

Prints usage information.

-in

Input file.

-out

Output txt file.

-roi

Region of interest. Required.

-resolution

Spatial resolution prior to upsampling. Required.