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A. Installation

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Javier Gonzalez-Castillo edited this page Jan 19, 2023 · 11 revisions

Required Packages

  • lemon_pipelines: originally available here. These pipelines had to be modified so they could run on our Biowulf environment. The modified version of the pipeline used in this work can be found at: https://github.com/nimh-sfim/lsd_pipelines_nih

  • mipav Version 5.4.2_amd64: you can download MIPAV from here. At the bottom of the page there is a section titled "Archived MIPAV Binary releases < 10.0.0". You can find the version we need there.

  • jist, jist-cruise, cbs tools for MIPAV: you can download it from here CBS Tools 3.0.8 + JIST-CRUISE 3.2 bundle

  • nipype: for this work, we used version 1.3.2 (to ensure functionality of the lemon pipelines)

  • fsl: version 5.0.10

  • freesurfer: version 5.3.0

  • ANTs: version 2.2.0

MIPAV & JIST Plugins

1. Install MIPAV

Although biowulf provides MIPAV as a module, for this project we need a much older version than those provided by the HPC team. For that reason we will have to install our own local copy. The version we need for this project in 5.4.2_amd64.

  1. You can find the installer for this version in: /data/SFIMJGC_Introspec/2023_fc_introspection/downloads/MIPAV/installMIPAV_5.4.2_amd64.bin.

  2. Open a terminal on an spersist node with graphical access (e.g., in no-machine or VNC)

  3. Run the installer

cd /data/SFIMJGC_Introspec/2023_fc_introspection/downloads/MIPAV/
chmod +x ./installMIPAV_5.4.2_amd64.bin
./installMIPAV_5.4.2_amd64.bin

NOTE: When asked where to install the sofware, please select /data/SFIMJGC_Introspec/2023_fc_introspection/sw/mipav

2. Install the JIST plugins in MIPAV

Similarly, we need to install an older version of these plugins. They are already available at /data/SFIMJGC_Introspec/2023_fc_introspection/downloads/JIST/JIST-2014Dec12-03-34PM.jar

  1. Open a terminal on an spersist node with graphical access (e.g., in no-machine or VNC)
cd /data/SFIMJGC_Introspec/2023_fc_introspection/sw/mipav
./mipav
  1. On the main MIPAV window go to Plugins --> Install Plugins

NOTE: If this is your first time opening mipav, the software will tell you that the plugins folder was missing and that you need to restart MIPAV. Follow those instructions. As a result of this, MIPAV will create a folder on your home directory /home/<your_user_name>/mipav/.

  1. On the Install Plugins window, press on Browse and in the new pop-up menus select the folder /data/SFIMJGC_Introspec/2023_fc_introspection/downloads/JIST and press ok.

  2. Select the JIST-2014Dec12-03-34PM.jar on the left list and press the right pointing arrow on the middle of the install plugin dialog to add it to the empty list on the right.

  3. Press Install Plugins. This operation is quite slow and it will throw some "plugin not found" messages on the terminal. That's ok as long as by the end of the installation process, you see a new menu item named JIST on the Plugins menu from the main MIPAV window.

  4. Exit MIPAV

3. Install the JIST-CRUISE plugins in MIPAV

Follow the same instructions as in Step 2 (above), but this time select the file JIST-CRUISE-2014Dec12-03-37PM.jar on the plugin installation dialog box.

Once you have install these plugins, exit MIPAV

LEMON Pre-processing Pipelines (Modified version for NIH Biowulf environment)

1. Clone the lemon pre-processing pipelines repo locally

  1. Open a terminal in an spersist node and create/enter target folder
cd /data/SFIMJGC_Introspec/2023_fc_introspection/code/
  1. Clone the pre-processing pipelines

git clone https://github.com/nimh-sfim/lsd_pipelines_nih.git

4. Create a local python environment based on the YAML file provided in this repository

[Add info here]

Clone this wiki locally