Dear Michael,
I try to install Python and Pysurfer following the instructions (using
*easy_install
-U pysurfer *and additional packages using*EPD*). 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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