Hi Alex, Thanks for your suggestion! I download Python 2.7 and install it. In my computer: ~/Library/Python, here are 3 version Python (2.3, 2.5, 2.6 ). there is no 2.7 ~/Library/Python. It reminds me create a directory in /Users/Kathy/library/Python/2.7. When I use easy_install -U Pysurfer, the error is : no Python/2.6 in Users/Kathy/library. It looks like it always search Python 2.6 even though I installed Python 2.7. Did I install Python 2.7 in wrong place?
Thanks Kathy On Fri, May 4, 2012 at 3:48 PM, Alexandre Gramfort < alexandre.gramf...@inria.fr> wrote: > 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 > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > > >> > 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 > >> > error > >> > but does not contain patient information, please contact the sender > and > >> > properly > >> > dispose of the e-mail. > >> > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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 > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > >
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