Threshold without GUI

Posted by vietducensam on Jul 03, 2017; 10:07am
URL: http://imagej.273.s1.nabble.com/Threshold-without-GUI-tp5019023.html

Hello, I am trying to use the ImageJ built-in threshold process in our Linux environment which have NO graphic. The macro is below: print('This is the macro_Tomo_etape2_v1'); open("$FilePath/B10_1_clearoutside_1.tif"); setAutoThreshold("Default"); run("Threshold..."); setThreshold(0, 30000); run("Convert to Mask", "method=Default background=Light"); run("Close"); saveAs("Tiff", "$FilePath/B10_1_clearoutside_1_thresholded.tif"); close(); However I have always the error shown below: No GUI detected. Falling back to headless mode. No GUI detected. Falling back to headless mode. Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0 Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release I have tried the headless mode in ImageJ and even the Xvfb but nothing works. Could you please help me. Thankyou in advance. PS: Sorry for my bad English