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
Hi Kathy, there is not an easy way to do this. The closest thing you could do would be to create an annotation with those 3 colors based on the thresholded sig maps. Let me know if you want instructions to do this. doug
On 05/02/2012 10:51 AM, keepmoon 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
Dear Doug,
Thank you for your reply soon. I would like to know further instructions for doing this.
Thanks
Best wishes
Kathy
On Wed, May 2, 2012 at 5:59 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Kathy, there is not an easy way to do this. The closest thing you could do would be to create an annotation with those 3 colors based on the thresholded sig maps. Let me know if you want instructions to do this. doug
On 05/02/2012 10:51 AM, keepmoon 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
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
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.
Dear Michael, Thank you for your answer! I will try it! but I have no knowledge about Python. I have some Matlab code. Maybe I first wait Doug's answer. If his answer is a little easier to understand for me, I will share here.
Thanks
Regards
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
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.
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 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
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.
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
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.
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
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.
Hi Michael and Alex,
Thanks for your suggestion about my question!
I am trying to install *Pysurfer* to solve my problem (load multiple overlays with different colors). I have already installed all the software following the instruction (three software (1) *epd-7.2-2-macosx-i386.dmg*; (2) *setuptools-0.6c11-py2.7.egg (md5);* (3) *python-2.7.3-macosx10.3.dmg*).
Now I test Pysurfer using command:
*Pysurfer fsaverage lh inflated*
It doesn’t work. The error is:
* *
% pysurfer fsaverage lh inflated
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/bin/pysurfer", line 5, in <module>
pkg_resources.run_script('pysurfer==0.3', 'pysurfer')
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 489, in run_script
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 1207, in run_script
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysurfer-0.3-py2.7.egg/EGG-INFO/scripts/pysurfer", line 9, in <module>
from surfer._commandline import parser
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysurfer-0.3-py2.7.egg/surfer/__init__.py", line 2, in <module>
from viz import Brain, TimeViewer
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysurfer-0.3-py2.7.egg/surfer/viz.py", line 19, in <module>
from enthought.traits.api import (HasTraits, Range, Int, Float, \
ImportError: No module named enthought.traits.api
Then I tried to install enthought.traits.api.
*% easy_install enthought.traits.api*
Searching for enthought.traits.api
Reading http://pypi.python.org/simple/enthought.traits.api/
Couldn't find index page for 'enthought.traits.api' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading http://pypi.python.org/simple/
No local packages or download links found for enthought.traits.api
error: Could not find suitable distribution for Requirement.parse('enthought.traits.api')
I didn’t find suitable answer to this question. Could you give me some suggestions?
Thanks
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
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.
hi,
this problem has been reported and fixed.
You should install the latest hot fit with:
https://github.com/nipy/PySurfer/zipball/master
then do from the folder:
python setup.py install
HTH
Alex
On Sat, May 5, 2012 at 10:09 PM, keepmoon keepmoon1224@googlemail.com wrote:
Hi Michael and Alex,
Thanks for your suggestion about my question!
I am trying to install Pysurfer to solve my problem (load multiple overlays with different colors). I have already installed all the software following the instruction (three software (1) epd-7.2-2-macosx-i386.dmg; (2) setuptools-0.6c11-py2.7.egg (md5); (3) python-2.7.3-macosx10.3.dmg).
Now I test Pysurfer using command:
Pysurfer fsaverage lh inflated
It doesn’t work. The error is:
% pysurfer fsaverage lh inflated
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/bin/pysurfer", line 5, in <module>
pkg_resources.run_script('pysurfer==0.3', 'pysurfer')
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 489, in run_script
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 1207, in run_script
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysurfer-0.3-py2.7.egg/EGG-INFO/scripts/pysurfer", line 9, in <module>
from surfer._commandline import parser
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysurfer-0.3-py2.7.egg/surfer/__init__.py", line 2, in <module>
from viz import Brain, TimeViewer
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysurfer-0.3-py2.7.egg/surfer/viz.py", line 19, in <module>
from enthought.traits.api import (HasTraits, Range, Int, Float, \
ImportError: No module named enthought.traits.api
Then I tried to install enthought.traits.api.
% easy_install enthought.traits.api
Searching for enthought.traits.api
Reading http://pypi.python.org/simple/enthought.traits.api/
Couldn't find index page for 'enthought.traits.api' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading http://pypi.python.org/simple/
No local packages or download links found for enthought.traits.api
error: Could not find suitable distribution for Requirement.parse('enthought.traits.api')
I didn’t find suitable answer to this question. Could you give me some suggestions?
Thanks
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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Hi Alex,
Thanks for your answer! Now it works!
Regards
Kathy
On Sat, May 5, 2012 at 10:13 PM, Alexandre Gramfort < alexandre.gramfort@inria.fr> wrote:
hi,
this problem has been reported and fixed.
You should install the latest hot fit with:
https://github.com/nipy/PySurfer/zipball/master
then do from the folder:
python setup.py install
HTH
Alex
On Sat, May 5, 2012 at 10:09 PM, keepmoon keepmoon1224@googlemail.com wrote:
Hi Michael and Alex,
Thanks for your suggestion about my question!
I am trying to install Pysurfer to solve my problem (load multiple overlays with different colors). I have already installed all the
software
following the instruction (three software (1) epd-7.2-2-macosx-i386.dmg;
(2)
setuptools-0.6c11-py2.7.egg (md5); (3) python-2.7.3-macosx10.3.dmg).
Now I test Pysurfer using command:
Pysurfer fsaverage lh inflated
It doesn’t work. The error is:
% pysurfer fsaverage lh inflated
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/bin/pysurfer", line 5, in <module>
pkg_resources.run_script('pysurfer==0.3', 'pysurfer')File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py",
line 489, in run_script
File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py",
line 1207, in run_script
File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysurfer-0.3-py2.7.egg/EGG-INFO/scripts/pysurfer",
line 9, in <module>
from surfer._commandline import parserFile
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysurfer-0.3-py2.7.egg/surfer/__init__.py",
line 2, in <module>
from viz import Brain, TimeViewerFile
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysurfer-0.3-py2.7.egg/surfer/viz.py",
line 19, in <module>
from enthought.traits.api import (HasTraits, Range, Int, Float, \ImportError: No module named enthought.traits.api
Then I tried to install enthought.traits.api.
% easy_install enthought.traits.api
Searching for enthought.traits.api
Reading http://pypi.python.org/simple/enthought.traits.api/
Couldn't find index page for 'enthought.traits.api' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading http://pypi.python.org/simple/
No local packages or download links found for enthought.traits.api
error: Could not find suitable distribution for Requirement.parse('enthought.traits.api')
I didn’t find suitable answer to this question. Could you give me some suggestions?
Thanks
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
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@nmr.mgh.harvard.edu
-
Alexandre Gramfort -
Douglas N Greve -
keepmoon -
Michael Waskom