Hi Kathy,
subprocess.check_output
was introduced in python 2.7. You use 2.6
I recommend to upgrade if possible.
Otherwise we need to fix this
Alex
On Fri, May 4, 2012 at 3:44 PM, keepmoon <keepmoon1...@googlemail.com> wrote:
> 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 <mwas...@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 <keepmoon1...@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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>> >
>> >
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>
>
>
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>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> properly
> dispose of the e-mail.
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