cdocutils.nodes document q)q}q(U nametypesq}q(Xgenerating 3-d modelsqNX%installing required packages (ubuntu)qNX(3d brain atlas reconstructor readme fileqNXgenerating documentationq NXgenerating caf datasetsq NXtroubleshootingq NuUsubstitution_defsq }q Uparse_messagesq]qcdocutils.nodes system_message q)q}q(U rawsourceqUU attributesq}q(Udupnamesq]qUlevelqKUidsq]qUbackrefsq]qUsourceqcdocutils.nodes reprunicode qX+/home/pmajka/4/doc/sphinx/source/README.rstqq }q!bUclassesq"]q#Unamesq$]q%Ulineq&MUtypeq'UERRORq(uUparentq)cdocutils.nodes list_item q*)q+}q,(hXSegmentation fault in Ubuntu 11.10 If the reconstructor crashes like that (numbers can vary): :: $ ./3dbar.sh ./3dbar.sh: line 17: 2296 Segmentation fault python bin/reconstructor/gui.py the reason can be a bug in the 'python-vtk' package installed in your system. Unfortunately there is no automated way to fix it - you have to do it manually: 1. Find a file named 'wxVTKRenderWindowInteractor.py'. It can be located in '/usr/share/pyshared/vtk/wx/' directory or in similar location: :: $ find / -name 'wxVTKRenderWindowInteractor.py' 2. Edit the file with your favourite ASCII editor. In the example editor 'vim' is used and it is assumed that the path to the file is '/usr/share/pyshared/vtk/wx/wxVTKRenderWindowInteractor.py': :: $ sudo vim /usr/share/pyshared/vtk/wx/wxVTKRenderWindowInteractor.py 3. Near 350th line of the file find a following line: :: d = '_%s_%s' % (d[2:], 'void_p') 4. Add '\0' characters to the line to make it like below: :: d = '_%s_%s\0' % (d[2:], 'void_p') 5. Save the modified file. 6. The bug should be fixed for now. Try running 3dBAR again. If this solution doesn't work - let us know.q-h)cdocutils.nodes bullet_list q.)q/}q0(hUh)cdocutils.nodes section q1)q2}q3(hUh)h1)q4}q5(hUh)hUsourceq6h Utagnameq7Usectionq8h}q9(h]q:h"]q;h]qah$]q?hauUlineq@KUdocumentqAhUchildrenqB]qC(cdocutils.nodes title qD)qE}qF(hX(3d Brain Atlas Reconstructor readme fileqGh)h4h6h h7UtitleqHh}qI(h]qJh"]qKh]qLh]qMh$]qNuh@KhAhhB]qOcdocutils.nodes Text qPX(3d Brain Atlas Reconstructor readme fileqQqR}qS(hhGh)hEubaubcdocutils.nodes paragraph qT)qU}qV(hXIn this file you can find a brief description of the 3D Brain Atlas Reconstructor software instalation and usage. Please visit the http://www.3dbar.org website for more detailed description.qWh)h4h6h h7U paragraphqXh}qY(h]qZh"]q[h]q\h]q]h$]q^uh@K hAhhB]q_(hPXIn this file you can find a brief description of the 3D Brain Atlas Reconstructor software instalation and usage. Please visit the q`qa}qb(hXIn this file you can find a brief description of the 3D Brain Atlas Reconstructor software instalation and usage. Please visit the qch)hUubcdocutils.nodes reference qd)qe}qf(hXhttp://www.3dbar.orgqgh}qh(UrefuriqiXhttp://www.3dbar.orgqjh]qkh]qlh]qmh"]qnh$]qouh)hUhB]qphPXhttp://www.3dbar.orgqqqr}qs(hUh)heubah7U referenceqtubhPX' website for more detailed description.quqv}qw(hX' website for more detailed description.qxh)hUubeubhT)qy}qz(hXIf you haven't done this already, please let us know that you are using 3D Brain Atlas Reconstructor by filling out short form available on http://service.3dbar.org/downloadForm . Thanks a lot.q{h)h4h6h h7hXh}q|(h]q}h"]q~h]qh]qh$]quh@K hAhhB]q(hPXIf you haven't done this already, please let us know that you are using 3D Brain Atlas Reconstructor by filling out short form available on qq}q(hXIf you haven't done this already, please let us know that you are using 3D Brain Atlas Reconstructor by filling out short form available on qh)hyubhd)q}q(hX%http://service.3dbar.org/downloadFormqh}q(UrefuriqX%http://service.3dbar.org/downloadFormqh]qh]qh]qh"]qh$]quh)hyhB]qhPX%http://service.3dbar.org/downloadFormqq}q(hUh)hubah7htubhPX . Thanks a lot.qq}q(hX . Thanks a lot.qh)hyubeubh1)q}q(hUh)h4h6h h7h8h}q(h]qh"]qh]qh]qU#installing-required-packages-ubuntuqah$]qhauh@KhAhhB]q(hD)q}q(hX%Installing required packages (Ubuntu)qh)hh6h h7hHh}q(h]qh"]qh]qh]qh$]quh@KhAhhB]qhPX%Installing required packages (Ubuntu)qq}q(hhh)hubaubh.)q}q(hUh)hh6h h7U bullet_listqh}q(UbulletqX*h]qh]qh]qh"]qh$]quh@KhAhhB]q(h*)q}q(hX[Installation in Ubuntu/Kubuntu 11.10 1. Install the Visualization Toolkit and other graphics libraries:: sudo apt-get install libvtk5.6 libvtk5-dev libvtk5.6-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti 2. Install python related packages:: sudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.8 3. Other packages:: sudo apt-get install potrace pstoedit python-setuptools python-epydoc 4. Install Sphinx:: sudo easy_install -U Sphinx qh)hh6Nh7U list_itemqh}q(h]qh"]qh]qh]qh$]quh@NhAhhB]q(hT)q}q(hX$Installation in Ubuntu/Kubuntu 11.10qh)hh6h h7hXh}q(h]qh"]qh]qh]qh$]quh@KhB]qhPX$Installation in Ubuntu/Kubuntu 11.10qхq}q(hhh)hubaubcdocutils.nodes enumerated_list q)q}q(hUh}q(UsuffixqU.h]qh]qh]qUprefixqUh"]qh$]qUenumtypeqUarabicquh)hhB]q(h*)q}q(hXInstall the Visualization Toolkit and other graphics libraries:: sudo apt-get install libvtk5.6 libvtk5-dev libvtk5.6-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti qh}q(h]qh"]qh]qh]qh$]quh)hhB]q(hT)q}q(hX@Install the Visualization Toolkit and other graphics libraries::qh)hh6h h7hXh}q(h]qh"]qh]qh]qh$]quh@KhB]qhPX?Install the Visualization Toolkit and other graphics libraries:qq}q(hX?Install the Visualization Toolkit and other graphics libraries:qh)hubaubcdocutils.nodes literal_block q)q}q(hXsudo apt-get install libvtk5.6 libvtk5-dev libvtk5.6-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-niftiqh)hh7U literal_blockqh}q(U xml:spacerUpreserverh]rh]rh]rh"]rh$]ruh@KhB]rhPXsudo apt-get install libvtk5.6 libvtk5-dev libvtk5.6-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-niftirr }r (hUh)hubaubeh7hubh*)r }r (hXInstall python related packages:: sudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.8 r h}r(h]rh"]rh]rh]rh$]ruh)hhB]r(hT)r}r(hX!Install python related packages::rh)j h6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhB]rhPX Install python related packages:rr }r!(hX Install python related packages:r"h)jubaubh)r#}r$(hXksudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.8r%h)j h7hh}r&(jjh]r'h]r(h]r)h"]r*h$]r+uh@KhB]r,hPXksudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.8r-r.}r/(hUh)j#ubaubeh7hubh*)r0}r1(hXZOther packages:: sudo apt-get install potrace pstoedit python-setuptools python-epydoc r2h}r3(h]r4h"]r5h]r6h]r7h$]r8uh)hhB]r9(hT)r:}r;(hXOther packages::r<h)j0h6h h7hXh}r=(h]r>h"]r?h]r@h]rAh$]rBuh@K"hB]rChPXOther packages:rDrE}rF(hXOther packages:rGh)j:ubaubh)rH}rI(hXEsudo apt-get install potrace pstoedit python-setuptools python-epydocrJh)j0h7hh}rK(jjh]rLh]rMh]rNh"]rOh$]rPuh@K$hB]rQhPXEsudo apt-get install potrace pstoedit python-setuptools python-epydocrRrS}rT(hUh)jHubaubeh7hubh*)rU}rV(hX1Install Sphinx:: sudo easy_install -U Sphinx rWh}rX(h]rYh"]rZh]r[h]r\h$]r]uh)hhB]r^(hT)r_}r`(hXInstall Sphinx::rah)jUh6h h7hXh}rb(h]rch"]rdh]reh]rfh$]rguh@K&hB]rhhPXInstall Sphinx:rirj}rk(hXInstall Sphinx:rlh)j_ubaubh)rm}rn(hXsudo easy_install -U Sphinxroh)jUh7hh}rp(jjh]rqh]rrh]rsh"]rth$]ruuh@K(hB]rvhPXsudo easy_install -U Sphinxrwrx}ry(hUh)jmubaubeh7hubeh7Uenumerated_listrzubeubh*)r{}r|(hXdInstallation in Ubuntu 10.10 and Ubuntu 11.04 1. Install the Visualization Toolkit and other graphics libraries:: sudo apt-get install libvtk5.4 libvtk5-dev libvtk5.4-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti 2. Install python related packages:: sudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.8 3. Other packages:: sudo apt-get install potrace pstoedit python-setuptools python-epydoc 4. Install Sphinx:: sudo easy_install -U Sphinx r}h)hh6Nh7hh}r~(h]rh"]rh]rh]rh$]ruh@NhAhhB]r(hT)r}r(hX-Installation in Ubuntu 10.10 and Ubuntu 11.04rh)j{h6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@K+hB]rhPX-Installation in Ubuntu 10.10 and Ubuntu 11.04rr}r(hjh)jubaubh)r}r(hUh}r(hU.h]rh]rh]rhUh"]rh$]rhhuh)j{hB]r(h*)r}r(hXInstall the Visualization Toolkit and other graphics libraries:: sudo apt-get install libvtk5.4 libvtk5-dev libvtk5.4-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti rh}r(h]rh"]rh]rh]rh$]ruh)jhB]r(hT)r}r(hX@Install the Visualization Toolkit and other graphics libraries::rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@K-hB]rhPX?Install the Visualization Toolkit and other graphics libraries:rr}r(hX?Install the Visualization Toolkit and other graphics libraries:rh)jubaubh)r}r(hXsudo apt-get install libvtk5.4 libvtk5-dev libvtk5.4-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-niftirh)jh7hh}r(jjh]rh]rh]rh"]rh$]ruh@K/hB]rhPXsudo apt-get install libvtk5.4 libvtk5-dev libvtk5.4-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-niftirr}r(hUh)jubaubeh7hubh*)r}r(hXInstall python related packages:: sudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.8 rh}r(h]rh"]rh]rh]rh$]ruh)jhB]r(hT)r}r(hX!Install python related packages::rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@K3hB]rhPX Install python related packages:rr}r(hX Install python related packages:rh)jubaubh)r}r(hXksudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.8rh)jh7hh}r(jjh]rh]rh]rh"]rh$]ruh@K5hB]rhPXksudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.8rr}r(hUh)jubaubeh7hubh*)r}r(hXZOther packages:: sudo apt-get install potrace pstoedit python-setuptools python-epydoc rh}r(h]rh"]rh]rh]rh$]ruh)jhB]r(hT)r}r(hXOther packages::rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@K8hB]rhPXOther packages:rr}r(hXOther packages:rh)jubaubh)r}r(hXEsudo apt-get install potrace pstoedit python-setuptools python-epydocrh)jh7hh}r(jjh]rh]rh]rh"]rh$]ruh@K:hB]rhPXEsudo apt-get install potrace pstoedit python-setuptools python-epydocrr}r (hUh)jubaubeh7hubh*)r }r (hX1Install Sphinx:: sudo easy_install -U Sphinx r h}r (h]rh"]rh]rh]rh$]ruh)jhB]r(hT)r}r(hXInstall Sphinx::rh)j h6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhB]r+hPXsudo easy_install -U Sphinxr,r-}r.(hUh)j"ubaubeh7hubeh7jzubeubh*)r/}r0(hXSInstallation in Ubuntu 10.04 1. Install the Visualization Toolkit and other graphics libraries:: sudo apt-get install libvtk5.2 libvtk5-dev libvtk5.2-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti 2. Install python related packages:: sudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.6 3. Other packages:: sudo apt-get install potrace pstoedit python-setuptools python-epydoc 4. Install Sphinx:: sudo easy_install -U Sphinx r1h)hh6Nh7hh}r2(h]r3h"]r4h]r5h]r6h$]r7uh@NhAhhB]r8(hT)r9}r:(hXInstallation in Ubuntu 10.04r;h)j/h6h h7hXh}r<(h]r=h"]r>h]r?h]r@h$]rAuh@KAhB]rBhPXInstallation in Ubuntu 10.04rCrD}rE(hj;h)j9ubaubh)rF}rG(hUh}rH(hU.h]rIh]rJh]rKhUh"]rLh$]rMhhuh)j/hB]rN(h*)rO}rP(hXInstall the Visualization Toolkit and other graphics libraries:: sudo apt-get install libvtk5.2 libvtk5-dev libvtk5.2-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti rQh}rR(h]rSh"]rTh]rUh]rVh$]rWuh)jFhB]rX(hT)rY}rZ(hX@Install the Visualization Toolkit and other graphics libraries::r[h)jOh6h h7hXh}r\(h]r]h"]r^h]r_h]r`h$]rauh@KChB]rbhPX?Install the Visualization Toolkit and other graphics libraries:rcrd}re(hX?Install the Visualization Toolkit and other graphics libraries:rfh)jYubaubh)rg}rh(hXsudo apt-get install libvtk5.2 libvtk5-dev libvtk5.2-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-niftirih)jOh7hh}rj(jjh]rkh]rlh]rmh"]rnh$]rouh@KEhB]rphPXsudo apt-get install libvtk5.2 libvtk5-dev libvtk5.2-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-niftirqrr}rs(hUh)jgubaubeh7hubh*)rt}ru(hXInstall python related packages:: sudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.6 rvh}rw(h]rxh"]ryh]rzh]r{h$]r|uh)jFhB]r}(hT)r~}r(hX!Install python related packages::rh)jth6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KIhB]rhPX Install python related packages:rr}r(hX Install python related packages:rh)j~ubaubh)r}r(hXksudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.6rh)jth7hh}r(jjh]rh]rh]rh"]rh$]ruh@KKhB]rhPXksudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.6rr}r(hUh)jubaubeh7hubh*)r}r(hXZOther packages:: sudo apt-get install potrace pstoedit python-setuptools python-epydoc rh}r(h]rh"]rh]rh]rh$]ruh)jFhB]r(hT)r}r(hXOther packages::rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KNhB]rhPXOther packages:rr}r(hXOther packages:rh)jubaubh)r}r(hXEsudo apt-get install potrace pstoedit python-setuptools python-epydocrh)jh7hh}r(jjh]rh]rh]rh"]rh$]ruh@KPhB]rhPXEsudo apt-get install potrace pstoedit python-setuptools python-epydocrr}r(hUh)jubaubeh7hubh*)r}r(hX1Install Sphinx:: sudo easy_install -U Sphinx rh}r(h]rh"]rh]rh]rh$]ruh)jFhB]r(hT)r}r(hXInstall Sphinx::rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KRhB]rhPXInstall Sphinx:rr}r(hXInstall Sphinx:rh)jubaubh)r}r(hXsudo easy_install -U Sphinxrh)jh7hh}r(jjh]rh]rh]rh"]rh$]ruh@KThB]rhPXsudo easy_install -U Sphinxrr}r(hUh)jubaubeh7hubeh7jzubeubh*)r}r(hXSInstallation in Ubuntu 9.10 1. Install the Visualization Toolkit and other graphics libraries:: sudo apt-get install libvtk5.2 libvtk5-dev libvtk5.2-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti 2. Install python related packages:: sudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.6 3. Other packages:: sudo apt-get install potrace pstoedit python-setuptools python-epydoc 4. Install Sphinx:: sudo easy_install -U Sphinx rh)hh6Nh7hh}r(h]rh"]rh]rh]rh$]ruh@NhAhhB]r(hT)r}r(hXInstallation in Ubuntu 9.10rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KWhB]rhPXInstallation in Ubuntu 9.10rr}r(hjh)jubaubh)r}r(hUh}r(hU.h]rh]rh]rhUh"]rh$]rhhuh)jhB]r(h*)r}r(hXInstall the Visualization Toolkit and other graphics libraries:: sudo apt-get install libvtk5.2 libvtk5-dev libvtk5.2-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti rh}r(h]rh"]rh]r h]r h$]r uh)jhB]r (hT)r }r(hX@Install the Visualization Toolkit and other graphics libraries::rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KYhB]rhPX?Install the Visualization Toolkit and other graphics libraries:rr}r(hX?Install the Visualization Toolkit and other graphics libraries:rh)j ubaubh)r}r(hXsudo apt-get install libvtk5.2 libvtk5-dev libvtk5.2-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-niftirh)jh7hh}r(jjh]rh]r h]r!h"]r"h$]r#uh@K[hB]r$hPXsudo apt-get install libvtk5.2 libvtk5-dev libvtk5.2-qt4 \ libvtk5-qt4-dev tk8.5 tk8.5-dev python-vtk libgtkgl2.0-1 \ libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-niftir%r&}r'(hUh)jubaubeh7hubh*)r(}r)(hXInstall python related packages:: sudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.6 r*h}r+(h]r,h"]r-h]r.h]r/h$]r0uh)jhB]r1(hT)r2}r3(hX!Install python related packages::r4h)j(h6h h7hXh}r5(h]r6h"]r7h]r8h]r9h$]r:uh@K_hB]r;hPX Install python related packages:r<r=}r>(hX Install python related packages:r?h)j2ubaubh)r@}rA(hXksudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.6rBh)j(h7hh}rC(jjh]rDh]rEh]rFh"]rGh$]rHuh@KahB]rIhPXksudo apt-get install python-gtkglext1 python-rsvg python-opengl \ python-numpy python-scipy python-wxgtk2.6rJrK}rL(hUh)j@ubaubeh7hubh*)rM}rN(hXZOther packages:: sudo apt-get install potrace pstoedit python-setuptools python-epydoc rOh}rP(h]rQh"]rRh]rSh]rTh$]rUuh)jhB]rV(hT)rW}rX(hXOther packages::rYh)jMh6h h7hXh}rZ(h]r[h"]r\h]r]h]r^h$]r_uh@KdhB]r`hPXOther packages:rarb}rc(hXOther packages:rdh)jWubaubh)re}rf(hXEsudo apt-get install potrace pstoedit python-setuptools python-epydocrgh)jMh7hh}rh(jjh]rih]rjh]rkh"]rlh$]rmuh@KfhB]rnhPXEsudo apt-get install potrace pstoedit python-setuptools python-epydocrorp}rq(hUh)jeubaubeh7hubh*)rr}rs(hX2Install Sphinx:: sudo easy_install -U Sphinx rth}ru(h]rvh"]rwh]rxh]ryh$]rzuh)jhB]r{(hT)r|}r}(hXInstall Sphinx::r~h)jrh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhhB]rhPXInstall Sphinx:rr}r(hXInstall Sphinx:rh)j|ubaubh)r}r(hXsudo easy_install -U Sphinxrh)jrh7hh}r(jjh]rh]rh]rh"]rh$]ruh@KjhB]rhPXsudo easy_install -U Sphinxrr}r(hUh)jubaubeh7hubeh7jzubeubeubeubh1)r}r(hUh)h4h6h h7h8h}r(h]rh"]rh]rh]rUgenerating-caf-datasetsrah$]rh auh@KohAhhB]r(hD)r}r(hXGenerating CAF datasetsrh)jh6h h7hHh}r(h]rh"]rh]rh]rh$]ruh@KohAhhB]rhPXGenerating CAF datasetsrr}r(hjh)jubaubhT)r}r(hXOnce the software is installed, you need to generate CAF representations of data of interest. For this you need to use parsers. We provide here the following parsers:rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KqhAhhB]rhPXOnce the software is installed, you need to generate CAF representations of data of interest. For this you need to use parsers. We provide here the following parsers:rr}r(hjh)jubaubh)r}r(hUh)jh6h h7jzh}r(hU.h]rh]rh]rhUh"]rh$]rhhuh@KuhAhhB]r(h*)r}r(hXgScalableBrainAtlas DB08 template (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=DB08) rh)jh6h h7hh}r(h]rh"]rh]rh]rh$]ruh@NhAhhB]rhT)r}r(hXfScalableBrainAtlas DB08 template (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=DB08)rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KuhB]r(hPX"ScalableBrainAtlas DB08 template (rr}r(hX"ScalableBrainAtlas DB08 template (rh)jubhd)r}r(hXChttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=DB08rh}r(UrefurirXChttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=DB08rh]rh]rh]rh"]rh$]ruh)jhB]rhPXChttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=DB08rr}r(hUh)jubah7htubhPX)r}r(hX)h)jubeubaubh*)r}r(hXiScalableBrainAtlas PHT00 template (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=PHT00) rh)jh6h h7hh}r(h]rh"]rh]rh]rh$]ruh@NhAhhB]rhT)r}r(hXhScalableBrainAtlas PHT00 template (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=PHT00)rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KxhB]r(hPX#ScalableBrainAtlas PHT00 template (rr}r(hX#ScalableBrainAtlas PHT00 template (rh)jubhd)r}r(hXDhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=PHT00rh}r(Urefurir XDhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=PHT00r h]r h]r h]r h"]rh$]ruh)jhB]rhPXDhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=PHT00rr}r(hUh)jubah7htubhPX)r}r(hX)h)jubeubaubh*)r}r(hXiScalableBrainAtlas WHS09 template (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=WHS09) rh)jh6h h7hh}r(h]rh"]rh]rh]rh$]ruh@NhAhhB]rhT)r }r!(hXhScalableBrainAtlas WHS09 template (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=WHS09)r"h)jh6h h7hXh}r#(h]r$h"]r%h]r&h]r'h$]r(uh@K{hB]r)(hPX#ScalableBrainAtlas WHS09 template (r*r+}r,(hX#ScalableBrainAtlas WHS09 template (r-h)j ubhd)r.}r/(hXDhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=WHS09r0h}r1(Urefurir2XDhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=WHS09r3h]r4h]r5h]r6h"]r7h$]r8uh)j hB]r9hPXDhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=WHS09r:r;}r<(hUh)j.ubah7htubhPX)r=}r>(hX)h)j ubeubaubh*)r?}r@(hXiScalableBrainAtlas WHS10 template (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=WHS10) rAh)jh6h h7hh}rB(h]rCh"]rDh]rEh]rFh$]rGuh@NhAhhB]rHhT)rI}rJ(hXhScalableBrainAtlas WHS10 template (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=WHS10)rKh)j?h6h h7hXh}rL(h]rMh"]rNh]rOh]rPh$]rQuh@K~hB]rR(hPX#ScalableBrainAtlas WHS10 template (rSrT}rU(hX#ScalableBrainAtlas WHS10 template (rVh)jIubhd)rW}rX(hXDhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=WHS10rYh}rZ(Urefurir[XDhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=WHS10r\h]r]h]r^h]r_h"]r`h$]rauh)jIhB]rbhPXDhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=WHS10rcrd}re(hUh)jWubah7htubhPX)rf}rg(hX)h)jIubeubaubh*)rh}ri(hX}ScalableBrainAtlas LPBA40_on_SRI24 template (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=LPBA40_on_SRI24) rjh)jh6h h7hh}rk(h]rlh"]rmh]rnh]roh$]rpuh@NhAhhB]rqhT)rr}rs(hX|ScalableBrainAtlas LPBA40_on_SRI24 template (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=LPBA40_on_SRI24)rth)jhh6h h7hXh}ru(h]rvh"]rwh]rxh]ryh$]rzuh@KhB]r{(hPX-ScalableBrainAtlas LPBA40_on_SRI24 template (r|r}}r~(hX-ScalableBrainAtlas LPBA40_on_SRI24 template (rh)jrubhd)r}r(hXNhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=LPBA40_on_SRI24rh}r(UrefurirXNhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=LPBA40_on_SRI24rh]rh]rh]rh"]rh$]ruh)jrhB]rhPXNhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=LPBA40_on_SRI24rr}r(hUh)jubah7htubhPX)r}r(hX)h)jrubeubaubh*)r}r(hXqScalableBrainAtlas RM_on_F99 template (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=RM_on_F99) rh)jh6h h7hh}r(h]rh"]rh]rh]rh$]ruh@NhAhhB]rhT)r}r(hXpScalableBrainAtlas RM_on_F99 template (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=RM_on_F99)rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhB]r(hPX'ScalableBrainAtlas RM_on_F99 template (rr}r(hX'ScalableBrainAtlas RM_on_F99 template (rh)jubhd)r}r(hXHhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=RM_on_F99rh}r(UrefurirXHhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=RM_on_F99rh]rh]rh]rh"]rh$]ruh)jhB]rhPXHhttp://scalablebrainatlas.incf.org/main/coronal3d.php?template=RM_on_F99rr}r(hUh)jubah7htubhPX)r}r(hX)h)jubeubaubh*)r}r(hXDthe Waxholm Space Atlas (the source mouse brain volumetric dataset) rh)jh6h h7hh}r(h]rh"]rh]rh]rh$]ruh@NhAhhB]rhT)r}r(hXCthe Waxholm Space Atlas (the source mouse brain volumetric dataset)rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhB]rhPXCthe Waxholm Space Atlas (the source mouse brain volumetric dataset)rr}r(hjh)jubaubaubh*)r}r(hXthe Waxholm Space Atlas (the source mouse brain volumetric dataset), another delineation (http://software.incf.org/software/waxholm-space/waxholm-space/LabeledAtlas0.5.1/file_download?file_field=file) rh)jh6h h7hh}r(h]rh"]rh]rh]rh$]ruh@NhAhhB]rhT)r}r(hXthe Waxholm Space Atlas (the source mouse brain volumetric dataset), another delineation (http://software.incf.org/software/waxholm-space/waxholm-space/LabeledAtlas0.5.1/file_download?file_field=file)rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhB]r(hPXZthe Waxholm Space Atlas (the source mouse brain volumetric dataset), another delineation (rr}r(hXZthe Waxholm Space Atlas (the source mouse brain volumetric dataset), another delineation (rh)jubhd)r}r(hXmhttp://software.incf.org/software/waxholm-space/waxholm-space/LabeledAtlas0.5.1/file_download?file_field=filerh}r(UrefurirXmhttp://software.incf.org/software/waxholm-space/waxholm-space/LabeledAtlas0.5.1/file_download?file_field=filerh]rh]rh]rh"]rh$]ruh)jhB]rhPXmhttp://software.incf.org/software/waxholm-space/waxholm-space/LabeledAtlas0.5.1/file_download?file_field=filerr}r(hUh)jubah7htubhPX)r}r(hX)h)jubeubaubh*)r}r(hXLSymmetrical Waxholm Space Atlas (the source mouse brain volumetric dataset) rh)jh6h h7hh}r(h]rh"]rh]rh]rh$]ruh@NhAhhB]rhT)r}r(hXKSymmetrical Waxholm Space Atlas (the source mouse brain volumetric dataset)rh)jh6h h7hXh}r(h]rh"]r h]r h]r h$]r uh@KhB]r hPXKSymmetrical Waxholm Space Atlas (the source mouse brain volumetric dataset)rr}r(hjh)jubaubaubh*)r}r(hXDPaxinos and Watson "The Rat Brain in Stereotaxic Coordinates" atlas rh)jh6h h7hh}r(h]rh"]rh]rh]rh$]ruh@NhAhhB]rhT)r}r(hXCPaxinos and Watson "The Rat Brain in Stereotaxic Coordinates" atlasrh)jh6h h7hXh}r(h]rh"]r h]r!h]r"h$]r#uh@KhB]r$hPXCPaxinos and Watson "The Rat Brain in Stereotaxic Coordinates" atlasr%r&}r'(hjh)jubaubaubh*)r(}r)(hXHFranklin and Paxinos "The Mouse Brain in Stereotaxic Coordinates" atlas r*h)jh6h h7hh}r+(h]r,h"]r-h]r.h]r/h$]r0uh@NhAhhB]r1hT)r2}r3(hXGFranklin and Paxinos "The Mouse Brain in Stereotaxic Coordinates" atlasr4h)j(h6h h7hXh}r5(h]r6h"]r7h]r8h]r9h$]r:uh@KhB]r;hPXGFranklin and Paxinos "The Mouse Brain in Stereotaxic Coordinates" atlasr<r=}r>(hj4h)j2ubaubaubh*)r?}r@(hXJThe Allen Mouse Brain Atlas (http://mouse.brain-map.org/atlas/index.html) rAh)jh6h h7hh}rB(h]rCh"]rDh]rEh]rFh$]rGuh@NhAhhB]rHhT)rI}rJ(hXIThe Allen Mouse Brain Atlas (http://mouse.brain-map.org/atlas/index.html)rKh)j?h6h h7hXh}rL(h]rMh"]rNh]rOh]rPh$]rQuh@KhB]rR(hPXThe Allen Mouse Brain Atlas (rSrT}rU(hXThe Allen Mouse Brain Atlas (rVh)jIubhd)rW}rX(hX+http://mouse.brain-map.org/atlas/index.htmlrYh}rZ(Urefurir[X+http://mouse.brain-map.org/atlas/index.htmlr\h]r]h]r^h]r_h"]r`h$]rauh)jIhB]rbhPX+http://mouse.brain-map.org/atlas/index.htmlrcrd}re(hUh)jWubah7htubhPX)rf}rg(hX)h)jIubeubaubeubhT)rh}ri(hXTo generate CAF dataset for data from ScalableBrainAtlas DB08 template execute the following commands in the root directory of the software:rjh)jh6h h7hXh}rk(h]rlh"]rmh]rnh]roh$]rpuh@KhAhhB]rqhPXTo generate CAF dataset for data from ScalableBrainAtlas DB08 template execute the following commands in the root directory of the software:rrrs}rt(hjjh)jhubaubh)ru}rv(hX%$ source setbarenv.sh $ make sba_DB08rwh)jh6h h7hh}rx(jjh]ryh]rzh]r{h"]r|h$]r}uh@KhAhhB]r~hPX%$ source setbarenv.sh $ make sba_DB08rr}r(hUh)juubaubhT)r}r(hXThe first line sets the path to the API and uses appropriate parser to download the data from SBA and do the transformation into the CAF dataset.rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]rhPXThe first line sets the path to the API and uses appropriate parser to download the data from SBA and do the transformation into the CAF dataset.rr}r(hjh)jubaubhT)r}r(hXYou can also generate that way CAF dataset for any of following SBA templates: ``PHT00``, ``WHS09``, ``WHS10``, ``LPBA40_on_SRI24`` and ``RM_on_F99`` just by replacing ``DB08`` with the name of the source template.rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]r(hPXOYou can also generate that way CAF dataset for any of following SBA templates: rr}r(hXOYou can also generate that way CAF dataset for any of following SBA templates: rh)jubcdocutils.nodes literal r)r}r(hX ``PHT00``rh}r(h]rh"]rh]rh]rh$]ruh)jhB]rhPXPHT00rr}r(hUh)jubah7UliteralrubhPX, rr}r(hX, rh)jubj)r}r(hX ``WHS09``rh}r(h]rh"]rh]rh]rh$]ruh)jhB]rhPXWHS09rr}r(hUh)jubah7jubhPX, rr}r(hX, rh)jubj)r}r(hX ``WHS10``rh}r(h]rh"]rh]rh]rh$]ruh)jhB]rhPXWHS10rr}r(hUh)jubah7jubhPX, rr}r(hX, rh)jubj)r}r(hX``LPBA40_on_SRI24``rh}r(h]rh"]rh]rh]rh$]ruh)jhB]rhPXLPBA40_on_SRI24rr}r(hUh)jubah7jubhPX and rr}r(hX and rh)jubj)r}r(hX ``RM_on_F99``rh}r(h]rh"]rh]rh]rh$]ruh)jhB]rhPX RM_on_F99rr}r(hUh)jubah7jubhPX just by replacing rr}r(hX just by replacing rh)jubj)r}r(hX``DB08``rh}r(h]rh"]rh]rh]rh$]ruh)jhB]rhPXDB08rr}r(hUh)jubah7jubhPX& with the name of the source template.rr}r(hX& with the name of the source template.rh)jubeubhT)r}r(hXIn order to generate that way CAF dataset for the Waxholm Space Atlas replace ``sba_DB08`` with ``whs_0.5``, ``whs_0.51`` (for another WHS delineation) or ```whs_0.5_symm`` (for symmetrical WHS).rh)jh6h h7hXh}r(h]r h"]r h]r h]r h$]r uh@KhAhhB]r(hPXNIn order to generate that way CAF dataset for the Waxholm Space Atlas replace rr}r(hXNIn order to generate that way CAF dataset for the Waxholm Space Atlas replace rh)jubj)r}r(hX ``sba_DB08``rh}r(h]rh"]rh]rh]rh$]ruh)jhB]rhPXsba_DB08rr}r(hUh)jubah7jubhPX with r r!}r"(hX with r#h)jubj)r$}r%(hX ``whs_0.5``r&h}r'(h]r(h"]r)h]r*h]r+h$]r,uh)jhB]r-hPXwhs_0.5r.r/}r0(hUh)j$ubah7jubhPX, r1r2}r3(hX, r4h)jubj)r5}r6(hX ``whs_0.51``r7h}r8(h]r9h"]r:h]r;h]r<h$]r=uh)jhB]r>hPXwhs_0.51r?r@}rA(hUh)j5ubah7jubhPX" (for another WHS delineation) or rBrC}rD(hX" (for another WHS delineation) or rEh)jubj)rF}rG(hX```whs_0.5_symm``rHh}rI(h]rJh"]rKh]rLh]rMh$]rNuh)jhB]rOhPX `whs_0.5_symmrPrQ}rR(hUh)jFubah7jubhPX (for symmetrical WHS).rSrT}rU(hX (for symmetrical WHS).rVh)jubeubhT)rW}rX(hX6To generate CAF dataset from Paxinos and Watson atlas (Paxinos, G. and Watson, C. (2007). The Rat Brain In Stereotaxic Coordinates. Elsevier, 6th edition.) you have to supply the parser with PDF file delivered with printed copy of the atlas. Execute the following command in the root directory of the software:rYh)jh6h h7hXh}rZ(h]r[h"]r\h]r]h]r^h$]r_uh@KhAhhB]r`hPX6To generate CAF dataset from Paxinos and Watson atlas (Paxinos, G. and Watson, C. (2007). The Rat Brain In Stereotaxic Coordinates. Elsevier, 6th edition.) you have to supply the parser with PDF file delivered with printed copy of the atlas. Execute the following command in the root directory of the software:rarb}rc(hjYh)jWubaubh)rd}re(hXK$ bash bin/parsers/paxinos_watson_rbisc/make_svg_from_pdf_rat.sh rfh)jh6h h7hh}rg(jjh]rhh]rih]rjh"]rkh$]rluh@KhAhhB]rmhPXK$ bash bin/parsers/paxinos_watson_rbisc/make_svg_from_pdf_rat.sh rnro}rp(hUh)jdubaubhT)rq}rr(hXYou have to replace ** with a valid path to the file mantioned above. The CAF dataset will be stored in the ``atlases/paxinos_watson_rbisc/caf-src`` directory.rsh)jh6h h7hXh}rt(h]ruh"]rvh]rwh]rxh$]ryuh@KhAhhB]rz(hPXYou have to replace r{r|}r}(hXYou have to replace r~h)jqubcdocutils.nodes emphasis r)r}r(hX **rh}r(h]rh"]rh]rh]rh$]ruh)jqhB]rhPX rr}r(hUh)jubah7UemphasisrubhPXV with a valid path to the file mantioned above. The CAF dataset will be stored in the rr}r(hXV with a valid path to the file mantioned above. The CAF dataset will be stored in the rh)jqubj)r}r(hX(``atlases/paxinos_watson_rbisc/caf-src``rh}r(h]rh"]rh]rh]rh$]ruh)jqhB]rhPX$atlases/paxinos_watson_rbisc/caf-srcrr}r(hUh)jubah7jubhPX directory.rr}r(hX directory.rh)jqubeubhT)r}r(hXIf the result of parsing does not satisfy you, you can edit slides derived from the PDF atlass manually with your favourite SVG editor.rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]rhPXIf the result of parsing does not satisfy you, you can edit slides derived from the PDF atlass manually with your favourite SVG editor.rr}r(hjh)jubaubhT)r}r(hXThe slides are located in ``atlases/paxinos_watson_rbisc/caf-src`` directory and named ``N_pretrace_v1.svg`` where N is the slide number. Once you have your slides edited execute in the root directory of the software:rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]r(hPXThe slides are located in rr}r(hXThe slides are located in rh)jubj)r}r(hX(``atlases/paxinos_watson_rbisc/caf-src``rh}r(h]rh"]rh]rh]rh$]ruh)jhB]rhPX$atlases/paxinos_watson_rbisc/caf-srcrr}r(hUh)jubah7jubhPX directory and named rr}r(hX directory and named rh)jubj)r}r(hX``N_pretrace_v1.svg``rh}r(h]rh"]rh]rh]rh$]ruh)jhB]rhPXN_pretrace_v1.svgrr}r(hUh)jubah7jubhPXm where N is the slide number. Once you have your slides edited execute in the root directory of the software:rr}r(hXm where N is the slide number. Once you have your slides edited execute in the root directory of the software:rh)jubeubh)r}r(hX$ make -f make_pw_rbisc.mkrh)jh6h h7hh}r(jjh]rh]rh]rh"]rh$]ruh@KhAhhB]rhPX$ make -f make_pw_rbisc.mkrr}r(hUh)jubaubhT)r}r(hXto reparse the edited slides.rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]rhPXto reparse the edited slides.rr}r(hjh)jubaubhT)r}r(hXSimilarly for Paxinos and Frnklin atlas (Paxinos, G. and Franklin, K. B. J. (2008). The Mouse Brain In Stereotaxic Coordinates. Elsevier, 3rd edition.) you have to execute:rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]rhPXSimilarly for Paxinos and Frnklin atlas (Paxinos, G. and Franklin, K. B. J. (2008). The Mouse Brain In Stereotaxic Coordinates. Elsevier, 3rd edition.) you have to execute:rr}r(hjh)jubaubh)r}r(hXO$ bash bin/parsers/paxinos_franklin_mbisc/make_svg_from_pdf_mouse.sh r h)jh6h h7hh}r (jjh]r h]r h]r h"]rh$]ruh@KhAhhB]rhPXO$ bash bin/parsers/paxinos_franklin_mbisc/make_svg_from_pdf_mouse.sh rr}r(hUh)jubaubhT)r}r(hXin the root directory of the software. The CAF dataset will be stored in the ``atlases/paxinos_franklin_mbisc/caf-src`` directory.rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]r(hPXMin the root directory of the software. The CAF dataset will be stored in the rr}r (hXMin the root directory of the software. The CAF dataset will be stored in the r!h)jubj)r"}r#(hX*``atlases/paxinos_franklin_mbisc/caf-src``r$h}r%(h]r&h"]r'h]r(h]r)h$]r*uh)jhB]r+hPX&atlases/paxinos_franklin_mbisc/caf-srcr,r-}r.(hUh)j"ubah7jubhPX directory.r/r0}r1(hX directory.r2h)jubeubhT)r3}r4(hX%To reparse the edited slides execute:r5h)jh6h h7hXh}r6(h]r7h"]r8h]r9h]r:h$]r;uh@KhAhhB]r<hPX%To reparse the edited slides execute:r=r>}r?(hj5h)j3ubaubh)r@}rA(hX$ make -f make_pf_mbisc.mkrBh)jh6h h7hh}rC(jjh]rDh]rEh]rFh"]rGh$]rHuh@KhAhhB]rIhPX$ make -f make_pf_mbisc.mkrJrK}rL(hUh)j@ubaubhT)rM}rN(hX&in the root directory of the software.rOh)jh6h h7hXh}rP(h]rQh"]rRh]rSh]rTh$]rUuh@KhAhhB]rVhPX&in the root directory of the software.rWrX}rY(hjOh)jMubaubhT)rZ}r[(hXGeneration of CAF dataset for The Allen Mouse Brain Atlas requires the Advanced Normalization Tools (ANTS; http://picsl.upenn.edu/ANTS/) installed. ANTS have to be availiable as shell commands (for an example by adding ANTS ``bin`` directory to environment value ``PATH``).r\h)jh6h h7hXh}r](h]r^h"]r_h]r`h]rah$]rbuh@KhAhhB]rc(hPXkGeneration of CAF dataset for The Allen Mouse Brain Atlas requires the Advanced Normalization Tools (ANTS; rdre}rf(hXkGeneration of CAF dataset for The Allen Mouse Brain Atlas requires the Advanced Normalization Tools (ANTS; rgh)jZubhd)rh}ri(hXhttp://picsl.upenn.edu/ANTS/rjh}rk(UrefurirlXhttp://picsl.upenn.edu/ANTS/rmh]rnh]roh]rph"]rqh$]rruh)jZhB]rshPXhttp://picsl.upenn.edu/ANTS/rtru}rv(hUh)jhubah7htubhPXY) installed. ANTS have to be availiable as shell commands (for an example by adding ANTS rwrx}ry(hXY) installed. ANTS have to be availiable as shell commands (for an example by adding ANTS rzh)jZubj)r{}r|(hX``bin``r}h}r~(h]rh"]rh]rh]rh$]ruh)jZhB]rhPXbinrr}r(hUh)j{ubah7jubhPX directory to environment value rr}r(hX directory to environment value rh)jZubj)r}r(hX``PATH``rh}r(h]rh"]rh]rh]rh$]ruh)jZhB]rhPXPATHrr}r(hUh)jubah7jubhPX).rr}r(hX).rh)jZubeubhT)r}r(hXATo generate CAF dataset from The Allen Mouse Brain Atlas execute:rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]rhPXATo generate CAF dataset from The Allen Mouse Brain Atlas execute:rr}r(hjh)jubaubh)r}r(hX $ source setbarenv.sh $ make abarh)jh6h h7hh}r(jjh]rh]rh]rh"]rh$]ruh@KhAhhB]rhPX $ source setbarenv.sh $ make abarr}r(hUh)jubaubhT)r}r(hX&in the root directory of the software.rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]rhPX&in the root directory of the software.rr}r(hjh)jubaubeubh1)r}r(hUh)h4h6h h7h8h}r(h]rh"]rh]rh]rUgenerating-3-d-modelsrah$]rhauh@KhAhhB]r(hD)r}r(hXGenerating 3-D modelsrh)jh6h h7hHh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]rhPXGenerating 3-D modelsrr}r(hjh)jubaubhT)r}r(hXtOnce you have a CAF of any dataset you can test the GUI for structure creation. To do it, in the main directory run:rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]rhPXtOnce you have a CAF of any dataset you can test the GUI for structure creation. To do it, in the main directory run:rr}r(hjh)jubaubh)r}r(hX $ ./3dbar.shrh)jh6h h7hh}r(jjh]rh]rh]rh"]rh$]ruh@KhAhhB]rhPX $ ./3dbar.shrr}r(hUh)jubaubhT)r}r(hXTand choose in the menu Atlas/Open and select *index.xml* file of chosen CAF dataset.rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]r(hPX-and choose in the menu Atlas/Open and select rr}r(hX-and choose in the menu Atlas/Open and select rh)jubj)r}r(hX *index.xml*rh}r(h]rh"]rh]r h]r h$]r uh)jhB]r hPX index.xmlr r}r(hUh)jubah7jubhPX file of chosen CAF dataset.rr}r(hX file of chosen CAF dataset.rh)jubeubhT)r}r(hX+To test, click the topmost label on the tree in the left panel and press *Perform reconstruction* button in the right panel. The reconstruction process will start. When it is finished, chose in the menu *Edit/Save Model*. It allows you to put it later in context by right click on the ontology tree.rh)jh6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@KhAhhB]r(hPXITo test, click the topmost label on the tree in the left panel and press rr}r (hXITo test, click the topmost label on the tree in the left panel and press r!h)jubj)r"}r#(hX*Perform reconstruction*r$h}r%(h]r&h"]r'h]r(h]r)h$]r*uh)jhB]r+hPXPerform reconstructionr,r-}r.(hUh)j"ubah7jubhPXj button in the right panel. The reconstruction process will start. When it is finished, chose in the menu r/r0}r1(hXj button in the right panel. The reconstruction process will start. When it is finished, chose in the menu r2h)jubj)r3}r4(hX*Edit/Save Model*r5h}r6(h]r7h"]r8h]r9h]r:h$]r;uh)jhB]r<hPXEdit/Save Modelr=r>}r?(hUh)j3ubah7jubhPXO. It allows you to put it later in context by right click on the ontology tree.r@rA}rB(hXO. It allows you to put it later in context by right click on the ontology tree.rCh)jubeubeubh1)rD}rE(hUh)h4h6h h7h8h}rF(h]rGh"]rHh]rIh]rJUgenerating-documentationrKah$]rLh auh@KhAhhB]rM(hD)rN}rO(hXGenerating documentationrPh)jDh6h h7hHh}rQ(h]rRh"]rSh]rTh]rUh$]rVuh@KhAhhB]rWhPXGenerating documentationrXrY}rZ(hjPh)jNubaubhT)r[}r\(hX+In order to generate documentation execute:r]h)jDh6h h7hXh}r^(h]r_h"]r`h]rah]rbh$]rcuh@MhAhhB]rdhPX+In order to generate documentation execute:rerf}rg(hj]h)j[ubaubh)rh}ri(hX $ source setbarenv.sh $ make docrjh)jDh6h h7hh}rk(jjh]rlh]rmh]rnh"]roh$]rpuh@MhAhhB]rqhPX $ source setbarenv.sh $ make docrrrs}rt(hUh)jhubaubhT)ru}rv(hXThe documentation for API can be viewed by opening *doc/api/html/index.html* and the documentation for 3dBAR graphic interface can be viewed by opening *doc/gui/html/index.html*.rwh)jDh6h h7hXh}rx(h]ryh"]rzh]r{h]r|h$]r}uh@MhAhhB]r~(hPX3The documentation for API can be viewed by opening rr}r(hX3The documentation for API can be viewed by opening rh)juubj)r}r(hX*doc/api/html/index.html*rh}r(h]rh"]rh]rh]rh$]ruh)juhB]rhPXdoc/api/html/index.htmlrr}r(hUh)jubah7jubhPXL and the documentation for 3dBAR graphic interface can be viewed by opening rr}r(hXL and the documentation for 3dBAR graphic interface can be viewed by opening rh)juubj)r}r(hX*doc/gui/html/index.html*rh}r(h]rh"]rh]rh]rh$]ruh)juhB]rhPXdoc/gui/html/index.htmlrr}r(hUh)jubah7jubhPX.r}r(hX.h)juubeubeubh2eubh6h h7h8h}r(h]rh"]rh]rh]rUtroubleshootingrah$]rh auh@M hAhhB]r(hD)r}r(hXTroubleshootingrh)h2h6h h7hHh}r(h]rh"]rh]rh]rh$]ruh@M hAhhB]rhPXTroubleshootingrr}r(hjh)jubaubh/eubh6h h7hh}r(hX*h]rh]rh]rh"]rh$]ruh@MhAhhB]rh+aubh6Nh7hh}r(h]rh"]rh]rh]rh$]ruh@NhAhhB]r(hT)r}r(hX"Segmentation fault in Ubuntu 11.10rh)h+h6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@MhB]rhPX"Segmentation fault in Ubuntu 11.10rr}r(hjh)jubaubhT)r}r(hX:If the reconstructor crashes like that (numbers can vary):rh)h+h6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@MhB]rhPX:If the reconstructor crashes like that (numbers can vary):rr}r(hjh)jubaubh)r}r(hX $ ./3dbar.shrh)h+h6h h7hh}r(jjh]rh]rh]rh"]rh$]ruh@MhB]rhPX $ ./3dbar.shrr}r(hUh)jubaubhT)r}r(hXR./3dbar.sh: line 17: 2296 Segmentation fault python bin/reconstructor/gui.pyrh)h+h6h h7hXh}r(h]rh"]rh]rh]rh$]ruh@MhB]rhPXR./3dbar.sh: line 17: 2296 Segmentation fault python bin/reconstructor/gui.pyrr}r(hjh)jubaubhT)r}r(hXthe reason can be a bug in the 'python-vtk' package installed in your system. Unfortunately there is no automated way to fix it - you have to do it manually:rh)h+h6h h7hXh}r(h]rh"]rh]r h]r h$]r uh@MhB]r hPXthe reason can be a bug in the 'python-vtk' package installed in your system. Unfortunately there is no automated way to fix it - you have to do it manually:r r }r (hjh)jubaubh)r }r (hUh}r (hU.h]r h]r h]r hUh"]r h$]r hhuh)h+hB]r (h*)r }r (hXFind a file named 'wxVTKRenderWindowInteractor.py'. It can be located in '/usr/share/pyshared/vtk/wx/' directory or in similar location: :: $ find / -name 'wxVTKRenderWindowInteractor.py' r h}r (h]r h"]r h]r h]r h$]r uh)j hB]r (hT)r }r (hXFind a file named 'wxVTKRenderWindowInteractor.py'. It can be located in '/usr/share/pyshared/vtk/wx/' directory or in similar location:r h)j h6h h7hXh}r (h]r h"]r h]r h]r! h$]r" uh@MhB]r# hPXFind a file named 'wxVTKRenderWindowInteractor.py'. It can be located in '/usr/share/pyshared/vtk/wx/' directory or in similar location:r$ r% }r& (hj h)j ubaubh)r' }r( (hX/$ find / -name 'wxVTKRenderWindowInteractor.py'r) h)j h6h h7hh}r* (jjh]r+ h]r, h]r- h"]r. h$]r/ uh@M!hB]r0 hPX/$ find / -name 'wxVTKRenderWindowInteractor.py'r1 r2 }r3 (hUh)j' ubaubeh7hubh*)r4 }r5 (hX Edit the file with your favourite ASCII editor. In the example editor 'vim' is used and it is assumed that the path to the file is '/usr/share/pyshared/vtk/wx/wxVTKRenderWindowInteractor.py': :: $ sudo vim /usr/share/pyshared/vtk/wx/wxVTKRenderWindowInteractor.py r6 h}r7 (h]r8 h"]r9 h]r: h]r; h$]r< uh)j hB]r= (hT)r> }r? (hXEdit the file with your favourite ASCII editor. In the example editor 'vim' is used and it is assumed that the path to the file is '/usr/share/pyshared/vtk/wx/wxVTKRenderWindowInteractor.py':r@ h)j4 h6h h7hXh}rA (h]rB h"]rC h]rD h]rE h$]rF uh@M$hB]rG hPXEdit the file with your favourite ASCII editor. In the example editor 'vim' is used and it is assumed that the path to the file is '/usr/share/pyshared/vtk/wx/wxVTKRenderWindowInteractor.py':rH rI }rJ (hj@ h)j> ubaubh)rK }rL (hXD$ sudo vim /usr/share/pyshared/vtk/wx/wxVTKRenderWindowInteractor.pyrM h)j4 h6h h7hh}rN (jjh]rO h]rP h]rQ h"]rR h$]rS uh@M*hB]rT hPXD$ sudo vim /usr/share/pyshared/vtk/wx/wxVTKRenderWindowInteractor.pyrU rV }rW (hUh)jK ubaubeh7hubh*)rX }rY (hXjNear 350th line of the file find a following line: :: d = '_%s_%s' % (d[2:], 'void_p') rZ h}r[ (h]r\ h"]r] h]r^ h]r_ h$]r` uh)j hB]ra (hT)rb }rc (hX2Near 350th line of the file find a following line:rd h)jX h6h h7hXh}re (h]rf h"]rg h]rh h]ri h$]rj uh@M-hB]rk hPX2Near 350th line of the file find a following line:rl rm }rn (hjd h)jb ubaubh)ro }rp (hX d = '_%s_%s' % (d[2:], 'void_p')rq h)jX h7hh}rr (jjh]rs h]rt h]ru h"]rv h$]rw uh@M1hB]rx hPX d = '_%s_%s' % (d[2:], 'void_p')ry rz }r{ (hUh)jo ubaubeh7hubh*)r| }r} (hXpAdd '\0' characters to the line to make it like below: :: d = '_%s_%s\0' % (d[2:], 'void_p') r~ h}r (h]r h"]r h]r h]r h$]r uh)j hB]r (hT)r }r (hX6Add '\0' characters to the line to make it like below:r h)j| h6h h7hXh}r (h]r h"]r h]r h]r h$]r uh@M4hB]r hPX5Add '0' characters to the line to make it like below:r r }r (hX6Add '\0' characters to the line to make it like below:r h)j ubaubh)r }r (hX"d = '_%s_%s\0' % (d[2:], 'void_p')r h)j| h7hh}r (jjh]r h]r h]r h"]r h$]r uh@M8hB]r hPX"d = '_%s_%s\0' % (d[2:], 'void_p')r r }r (hUh)j ubaubeh7hubh*)r }r (hXSave the modified file. r h}r (h]r h"]r h]r h]r h$]r uh)j hB]r hT)r }r (hXSave the modified file.r h)j h6h h7hXh}r (h]r h"]r h]r h]r h$]r uh@M;hB]r hPXSave the modified file.r r }r (hj h)j ubaubah7hubh*)r }r (hXfThe bug should be fixed for now. Try running 3dBAR again. If this solution doesn't work - let us know.r h}r (h]r h"]r h]r h]r h$]r uh)j hB]r hT)r }r (hXfThe bug should be fixed for now. Try running 3dBAR again. If this solution doesn't work - let us know.r h)j h6h h7hXh}r (h]r h"]r h]r h]r h$]r uh@M>hB]r hPXfThe bug should be fixed for now. Try running 3dBAR again. If this solution doesn't work - let us know.r r }r (hj h)j ubaubah7hubeh7jzubeubhB]r hT)r }r (hUh}r (h]r h"]r h]r h]r h$]r uh)hhB]r hPX#Inconsistent literal block quoting.r r }r (hUh)j ubah7hXubah7Usystem_messager ubaUcurrent_sourcer NU decorationr NUautofootnote_startr KUnameidsr }r (hjhhhh>h jKh jh juhB]r (cdocutils.nodes comment r )r }r (hX -*- rest -*-r h)hh6h h7Ucommentr h}r (jjh]r h]r h]r h"]r h$]r uh@KhAhhB]r hPX -*- rest -*-r r }r (hUh)j ubaubj )r }r (hXvim:syntax=restr h)hh6h h7j h}r (jjh]r h]r h]r h"]r h$]r uh@KhAhhB]r hPXvim:syntax=restr r }r (hUh)j ubaubh4ehUU transformerr NU footnote_refsr }r Urefnamesr }r Usymbol_footnotesr ]r Uautofootnote_refsr ]r Usymbol_footnote_refsr ]r U citationsr ]r hAhU current_liner NUtransform_messagesr ]r Ureporterr NUid_startr KU autofootnotesr ]r U citation_refsr }r Uindirect_targetsr ]r Usettingsr (cdocutils.frontend Values r or }r (Ufootnote_backlinksr KUrecord_dependenciesr NU rfc_base_urlr Uhttp://tools.ietf.org/html/r U tracebackr Upep_referencesr NUstrip_commentsr! 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