[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.