I didn't want to spend time changing settings etc. Instead I wrote this in PowerShell and it works now. For anyone out there having any issues with the script you can use the below
$Counters = @(
"\Processor(_Total)\% Processor Time",
"\LogicalDisk(_Total)\Disk Read Bytes/sec",
"\LogicalDisk(_Total)\Disk Write Bytes/sec",
"\LogicalDisk(_Total)\Disk Reads/sec",
"\LogicalDisk(_Total)\Disk Writes/sec",
"\Database(svchost)\Log Bytes Write/sec"
)
# Continuous monitoring with a specified sample interval
$Interval = 1 # seconds
$FilePath = "C:\MigrationMetrics\output.csv"
Get-Counter -Counter $Counters -Continuous -Interval $SampleInterval | Export-Counter -Path $FilePath -FileFormat CSV