Connectome mapper on Ubuntu

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1 Neurodebian Ubuntu12.04 Connectome mapper Ubuntu 2 2 Neurodebian 2 3 apt-get Connectome Viewer FSL MRtrix Java Lapack Connectome mapper git apt-get Diffusion Toolkit Freesurfer Camino Camino-Trackvis converter MITK MITK Diffusion bashrc

........................................ 5 4 apt-get 5 4.1 Diffusion Toolkit......................................... 5 4.2 Freesurfer............................................. 6 4.3 Camino.............................................. 7 4.

2 1 Ubuntu Nipype Connectome mapper Connectome mapper Ubuntu Neurodebian apt-get.bashrc $.bashrc #.bashrc # SOFT=/usr/local/hogehoge Lin4Neuro Freesurfer Diffusion Toolkit Connectome mapper Lin4Neuro Diffusion toolkit Freesurfer ( ) 1 Ubuntu Ubuntu 64bit bash 2 Neurodebian Neurodebian

html Ubuntu Neurodebian apt-get.bashrc $.bashrc #.

3 3 apt-get 3 $ wget -O- \ sudo tee /etc/apt/sources.list.d/neurodebian.sources.list $ sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9 apt-get update $ sudo apt-get update 3 apt-get 3.1 Connectome Viewer Connectome viewer $ sudo apt-get install connectomeviewer 3.2 FSL $ sudo apt-get install fsl fslview fslview-doc ~/.bashrc ~/.bashrc (~).bashrc #FSL. /etc/fsl/fsl.sh

edu 2649A5A9 apt-get update $ sudo apt-get update 3 apt-get 3.

4 3 apt-get MRtrix $ sudo apt-get install mrtrix ~/.bashrc #MRtrix export MRTRIX=/usr/lib/mrtrix/bin 3.4 Java Camino Oracle Java java-7 $ sudo add-apt-repository ppa:webupd8team/java $ sudo apt-get update $ sudo apt-get install oracle-java7-installer $ sudo apt-get install oracle-java7-set-default 3.5 Lapack Camino-Trackvis converter Lapack $ sudo apt-get install libblas-dev liblapack-dev libatlas-base-dev 3.6 Connectome mapper

4 Java Camino Oracle Java java-7 $ sudo add-apt-repository ppa:webupd8team/java $ sudo apt-get update $ sudo

5 4 apt-get 5 $ sudo apt-get install libboost-program-options-dev libnifti-dev libblitz0-dev $ sudo apt-get install libboost-program-options git $ sudo apt-get install git 4 apt-get apt-get 4.1 Diffusion Toolkit Sign up Diffusion Toolkit Linux (64-bit) Diffusion_Toolkit_v _x86_64.tar.gz foo Downloads /usr/local tar xvzf E(x)tract, (v)erbose, g(z)ip, (f)ile gzip $ cd /usr/local $ sudo tar xvzf /home/foo/diffusion_toolkit_v _x86_64.tar.gz /usr/local ~/.bashrc

6 4 apt-get 6 #Diffusion toolkit export DTDIR=/usr/local/dtk export DSI_PATH=/usr/local/dtk/matrices 4.2 Freesurfer freesurfer-linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz /usr/local Cent OS6 Ubuntu Web wget foo Downloads $ cd /home/foo/downloads $ wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/ freesurfer-linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz ( 2 1 ) $ cd /usr/local $ sudo tar xvzf /home/foo/downloads/ freesurfer-linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz ( 2 1 ) Freesurfer Registration # CUT HERE foo@example.com 1234 *St0rinGs. # CUT HERE

edu/pub/dist/freesurfer/5.3.0/ freesurfer-linux-centos4_x86_64-stable-pub-v5.3.0.tar.

7 4 apt-get 7 foo@example.com 1234 *St0rinGs..license.license ls -a.license /usr/local/freesurfer $ cd # $ sudo cp.license /usr/local/freesurfer ~/.bashrc #Freesurfer export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh 4.3 Camino camino camino-code-163f67cbf550560aa351b3d0a3bbbd7a22863cb4.zip camino $ unzip camino-code-xxxx(version number) $ cd camino-code-xxxx(version number) $ make $ cd.. $ mv camino-code-xxxx(version number) camino $ sudo cp -r camino /usr/local

net/projects/camino/files/latest/download camino 2014 3 3 camino-code-163f67cbf550560aa351b3d0a3bbbd7a22863cb4.

8 4 apt-get ~/.bashrc #Camino export MANPATH=/usr/local/camino/man:$MANPATH export CAMINODIR=/usr/local/camino/bin 4.4 Camino-Trackvis converter camino-trackvis tar.bz2 tar xvjf xvzf j j bzip $ tar xvjf camino-trackvis tar.bz2 $ cd camino-trackvis tar.bz2 $./build.sh $ cd.. $ sudo cp -r camino-trackvis /usr/local ~/.bashrc #Camino-trackvis export CAMINO2TRK=/usr/local/camino-trackvis /bin 4.5 MITK MITK linux64.tar.gz wget

bz2 tar xvjf xvzf j j bzip $ tar xvjf camino-trackvis-0.2.8.1.tar.bz2 $ cd camino-trackvis-0.2.8.1.tar.bz2 $./build.sh $ cd.

9 4 apt-get 9 $ cd /home/foo/downloads $ wget MITK linux64.tar.gz ( 2 1 ) $ cd /usr/local $ sudo tar xvzf /home/foo/downloads/mitk linux64.tar.gz ~/.bashrc #MITK export MITK=/usr/local/MITK linux MITK Diffusion MITK MITK-Diffusion linux64 wget $ cd /home/foo/downloads $ wget Linux/MITK-Diffusion linux64.tar.gz ( 2 1 ) $ cd /usr/local $ sudo tar xvzf /home/foo/downloads/mitk-diffusion linux64.tar.gz ~/.bashrc #MITK Diffusion export MITKDIFFUSION=/usr/local/MITK-Diffusion linux64

mitk.org/diffusionimaging#downloads MITK-Diffusion-2013.09.04-linux64 wget $ cd /home/foo/downloads $ wget http://mitk.org/download/releases/mitk-diffusion-2013.

10 4 apt-get ~/.bashrc #Update PATH export PATH="${DTDIR}:${MRTRIX}:${CAMINODIR}:${CAMINO2TRK}: ${MITK}:${MITKDIFFUSION}:${PATH}" 4.8.bashrc.bashrc FSL Freesurfer

11 4 apt-get 11 #FSL. /etc/fsl/fsl.sh #MRtrix export MRTRIX=/usr/lib/mrtrix/bin #Diffusion toolkit export DTDIR=/usr/local/dtk export DSI_PATH=/usr/local/dtk/matrices #Freesurfer export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh #Camino export MANPATH=/usr/local/camino/man:$MANPATH export CAMINODIR=/usr/local/camino/bin #Camino-trackvis export CAMINO2TRK=/usr/local/camino-trackvis /bin #MITK export MITK=/usr/local/MITK linux64 #MITK Diffusion export MITKDIFFUSION=/usr/local/MITK-Diffusion linux64 #Update PATH export PATH="${DTDIR}:${MRTRIX}:${CAMINODIR}:${CAMINO2TRK}: ${MITK}:${MITKDIFFUSION}:${PATH}" 4.9.bashrc $..bashrc

FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.

12 5 Connectome mapper Nipype Nipype Connectome mapper modify $ cd # $ git clone git://github.com/lts5/nipype.git $ cd nipype $ sudo python setup.py install Connectome mapper 5 Connectome mapper cmp_nipype beta.tar.gz git $ cd # $ git clone git://github.com/lts5/cmp_nipype.git $ cd cmp_nipype $ sudo python setup.py install Connectome mapper 5.1 Connectome mapper $ connectomemapper 1 6 Connectome mapper

com/lts5/cmp_nipype/releases cmp_nipype-2.1.0-beta.tar.gz git $ cd # $ git clone git://github.com/lts5/cmp_nipype.git $ cd cmp_nipype $ sudo python setup.

6 13 1 connectome mapper 6.1 http://cmtk.org/datasets/rawdata/ Connectome mapper project01_dsi.tar.gz connectomemapper $ tar xvzf project01_dsi.tar.gz $ connectomemapper 6.

13 connectome mapper Connectome mapper project01_dsi.tar.gz connectomemapper $ tar xvzf project01_dsi.tar.gz $ connectomemapper 6.2 Mapper File --> New Connectome data... 2 Browse... project01_dsi/connectome_001/tp1 3 Check input data 4 Inputs check finished successfully. Connectome 5 Connectome mapper Map Connectome!

15 Connectome

DCL intro Manual for Ubuntu12.04

DCL intro Manual for Ubuntu12.04 ubnutu 12.04 2013/Sep/15 i 1 1 2 ubuntu 2 3 3 3.1........................................... 3 3.2........................................ 3 3.3 gedit........................................... 4 3.4........................................