Upgrade instructions for v2.1.6-1, adding Schiz Bull 2008 anatomical scans and segmentation to IR (cs_schizbull2008).  Scripts are in NITRCSRC/feddata2/cs_schizbull2008/.

PACKAGE INSTALLATION
--------------------

1) Install Pyxnat:
  yum install python-setuptools
  yum install python-lxml
  yum install python-httplib2
  yum install python26-httplib2
  yum install python-nose python26-nose
  yum install python26-devel
  yum install libxml2-devel
  yum install libxslt-devel

  wget http://lxml.de/files/lxml-2.3.2.tgz
  tar zxvf lxml-2.3.2.tgz 
  cd lxml-2.3.2
  python26 setup.py build
  python26 setup.py install

Next you can try the easy install of pyxnat, but the web site doesn't 
recommend it for some obscure reason we don't care about.
  easy_install .prefix /usr/local pyxnat
The do recommend the manual install, but that fails on lxml and httplib2 dependencies depending on if you us
python or python26 to run the setup script.
  #  wget http://pypi.python.org/packages/source/p/pyxnat/pyxnat-0.9.2.tar.gz#md5=709dee52d54773721f267bc4fd9929a4
  #  tar -xvzf pyxnat-0.9.2.tar.gz
  #  cd pyxnat-0.9.2
  #  python26 setup.py build
  #  python26 setup.py install

2) For PIL, I think there are yum packages:
  yum install python-imaging python26-imaging
 
3) To install the nibabel we can try to use easy_install nibabel, 
but it wants numpy installed first, so try that first:
  yum install python26-numpy
Then:
  wget http://pypi.python.org/packages/source/n/nibabel/nibabel-1.1.0.tar.gz#md5=ba67801b80481171a7a583177d74d729
  tar zxvf nibabel-1.1.0.tar.gz 
  python26 setup.py build
  python26 setup.py install


4) Create a private project called cs_schizbull08 (this already exists on production)
5) Add the appropriate users to the list of Owners in a project.  (Note that in test when a new project was created, it was created with Guest as the owner.)




SCHEMA UPDATE
-------------

Add candi_share.xsd to XNAT, then add ir:CandiShareSegData as Segmentation/Segmentations (see XNAT_schema_update.txt).




UPLOAD
------

Set environment variables:

    XNAT_URI: base URI for the target XNAT  (ex http://nova.crbs.ucsd.edu:8084/ir)
    XNAT_USER: the uploading XNAT user
    XNAT_PASSWORD: the password for the uploading user

Download from NITRC (http://www.nitrc.org/frs/?group_id=377) and unpack:

    From release Img+Seg_V1.1:

        SchizBull_2008_BPDwoPsy_segimg.tar.gz
        SchizBull_2008_BPDwPsy_segimg.tar.gz
        SchizBull_2008_HC_segimg.tar.gz
        SchizBull_2008_SS_segimg.tar.gz

  1) Create the working directory
       cd /opt
       mkdir /candi
       cd candi

  2) Download the SchizBull data files from NITRC.  
       - Open http://www.nitrc.org/frs/?group_id=377
       - In the Img+Seg_V1.1 release download the following:
            SchizBull_2008_BPDwoPsy_segimg.tar.gz
            SchizBull_2008_BPDwPsy_segimg.tar.gz
            SchizBull_2008_HC_segimg.tar.gz
            SchizBull_2008_SS_segimg.tar.gz

      
  3) Unarchive the data files
       tar -xvzf SchizBull_2008_BPDwoPsy_segimg.tar.gz
       tar -xvzf SchizBull_2008_BPDwPsy_segimg.tar.gz
       tar -xvzf SchizBull_2008_HC_segimg.tar.gz
       tar -xvzf SchizBull_2008_SS_segimg.tar.gz


  4) copy the FreeSurferColorLUT.txt file to your current directory
       cp .../NITRCSRC/feddata2/cs_schizbull2008/FreeSurferColorLUT.txt .

  5) Execute the upload scripts
       
       .../NITRCSRC/feddata2/cs_schizbull2008/upload 
       .../NITRCSRC/feddata2/cs_schizbull2008/create_snapshots 
