[Brains-users] Problems with tissue class models due to dark T1 images

[Kevin Berne]

Hello,
Thank you very much for sending me the thresholding script along with the explanation of it. Since I myself sadly have no idea how to run the mentioned script under Cygwin I would like to ask you to perhaps describe a process through which I might be able to get the same results manually, if that process exists. I know it has already been described what the script does exactly, but I am unable to translate that into anything that I might be able to perform manually. So, if there is any way to do it manually, please guide me through it. If anyone knows how to do it and finds the time to write it down, I would be very grateful. If anyone even knows how to actually run the script under Cygwin, that would be even better...
By the way, we do not have PD images, so the T1 and T2 images are the only things to work with.
Finally, I had some time ago raised the question whether resampling the images with odd values (356x356x292 for example) to prevent a cut-off-effect we have been experiencing actually affects the measuring process later on. Since I still do not know the answer, I would still appreciate it if anyone knew anything about that matter.
Thank you again,
Kevin Berne
Central Institute of Mental Health http://www.zi-mannheim.de
Department of Neuropsychology D-68159 Mannheim J5
and Clinical Psychology  
 
 

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