How to activate site setting option in powershell?

Try this script

 $templateNamesToKeep = "STS#0","PROJECTSITE#0","BLOG#0"

 Start-SPAssignment -Global
 $web = Get-SPWeb <URL of site> 

 # get the existing web templates from the site that will be filtered down 
 # 1033 is the locale id for English US (en-us), be sure to change to your locale 
 $existingWebTemplates = $web.GetAvailableWebTemplates(1033) 
 $newWebTemplates = New-Object "System.Collections.ObjectModel.Collection[Microsoft.SharePoint.SPWebTemplate]"

 # filter existing web templates and only keep if in the list of template names to keep 
 $newWebTemplates = $existingWebTemplates | Where-Object {$_.name -in $templateNamesToKeep} 
 $web.SetAvailableWebTemplates($newWebTemplates, 1033) 
 $web.Update() 

 Stop-SPAssignment -Global 

at $templateNamesToKeep define the template that you need to only use for subsites.

For more details check Set PageLayouts and Site Templates Settings in SharePoint 2013 using PowerShell