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For some demand, I am using MathMLForm for all output

SetOptions["stdout", FormatType -> MathMLForm]

But this effect the syntax error format as well.(it's hard to understand and non-meaningful sometime in MathMLForm)

Then I tried bollwed, but syntax error message is still in MathMLForm

SetOptions["stdout", FormatType -> MathMLForm];
SetOptions["stderr", FormatType -> OutputForm];

So how could I change FormatType for output and Syntax error separately ? Thanks!

BTW : I am using version 9 under ubuntu 14.04 (32 bit)

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Not entirely sure I understand your problem but does this work for you? SetOptions[$FrontEndSession, AutoStyleOptions -> {"SyntaxErrorStyle" -> Directive[FontColor -> RGBColor[1, 0, 0], FontWeight -> Bold]}] –  Mike Honeychurch May 5 at 11:24
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