Dear Michael,

I try to install Python and Pysurfer following the instructions (using easy_install -U pysurfer  and  additional packages usingEPD). It didn't show error during the install process. Now I want to test it.

 In Terminal I typed:

Pysurfer fsaverage lh infalted
 then it shows following:

Traceback (most recent call last):
  File "/usr/local/bin/pysurfer", line 5, in <module>
    pkg_resources.run_script('pysurfer==0.3', 'pysurfer')
  File "/Library/Python/2.6/site-packages/setuptools-0.6c11-py2.6.egg/pkg_resources.py", line 489, in run_script
    
  File "/Library/Python/2.6/site-packages/setuptools-0.6c11-py2.6.egg/pkg_resources.py", line 1207, in run_script
    # we assume here that our metadata may be nested inside a "basket"
  File "/Library/Python/2.6/site-packages/pysurfer-0.3-py2.6.egg/EGG-INFO/scripts/pysurfer", line 9, in <module>
    from surfer._commandline import parser
  File "/Library/Python/2.6/site-packages/pysurfer-0.3-py2.6.egg/surfer/__init__.py", line 1, in <module>
    from io import Surface
  File "/Library/Python/2.6/site-packages/pysurfer-0.3-py2.6.egg/surfer/io.py", line 3, in <module>
    from subprocess import check_output
ImportError: cannot import name check_output



This means I didn't install successfully or where is wrong? The computer that I use is MacBook.


Thanks for your help!

Kathy





On Wed, May 2, 2012 at 6:32 PM, Michael Waskom <mwaskom@stanford.edu> wrote:
Hi,

If you're somewhat handy with Python, you can use PySurfer for this.
See this example:
http://pysurfer.github.com/auto_examples/plot_fmri_conjunction.html

Best,
Michael

On Wed, May 2, 2012 at 7:51 AM, keepmoon <keepmoon1224@googlemail.com> wrote:
> Dear all,
>
> I search my question before I post it. I did find similar questions, but
> didn't find answer. I want to overlay two files with different colors. For
> example, one is sig1.mgh from cortical thickness, the other is sig2.mgh from
> area. I want to use tksurfer overlaying them with three colors: red is
> significant regions of thickness; blue is significant regions of area; green
> is overlap significant regions of thickness and area.
>
> I tried to use the following command:
>
> tksurfer fsaverage lh inflated -annot aparc.annot -fthresh 2 -overlay
> sig1.mgh  -overlay sig2.mgh
>
> It just can display sig1.mgh or sig2.mgh, but can't display two together. In
> addition, I don't know how to control overlap and other regions color.
>
> Anyone knows how to do this?
>
> Any help will be appreciated!
>
> Thanks in advance!
>
> Kathy
>
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