[Freesurfer] copy of pbsubmit
Hi I am trying to setup a local pc as cluster to debug trac-all. Is it possible to get a copy of pbsubmit? I think I could use it as wrapper fro qsub on my pc. Best regards Knut J ___ 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.
Re: [Freesurfer] load multiple overlays with different colors
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
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
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
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
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 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
> 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.
Re: [Freesurfer] load multiple overlays with different colors
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 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
>
> 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
>
> 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
>
> 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
>
> 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 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
>> 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
Re: [Freesurfer] load multiple overlays with different colors
Hi Alex,
Thanks for your answer! Now it works!
Regards
Kathy
On Sat, May 5, 2012 at 10:13 PM, Alexandre Gramfort <
alexandre.gramf...@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
> 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
> >
> > 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
> >
> > 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
> >
> > 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
> >
> > 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
> 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
> >> 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
> >
Re: [Freesurfer] tracula
Hi Carolina - Tracula is not an exploratory method for tractography from any seed region of your choice. It reconstructs a specific set of 18 tracts. http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract a.y On Fri, 4 May 2012, carolina.mr wrote: > Hello, > > Is it possible to track fibers with TRACULA from the cortical parcelation > masks obtained from recon-all or do we have to use the white matter > parcelation to do so? > Another question: if I use QDEC to find the areas with significant > difference in the cortical tickness between two groups, is it possible to > use those ROI's to launch the fiber track with TRACULA? > > Thank you, > Carolina Rimkus > ___ 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.
