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.gramfort@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 keepmoon1224@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 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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